Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 2
  • Time
  • Show
Clear All
new posts
Previous 1 2 template Next
  • d_t_nguyen
    Member
    • Jun 2013
    • 13
    #1

    Problem installing UMAKE

    Hi everyone, I am trying to install UMAKE following this instruction http://genome.sph.umich.edu/wiki/UMAKE#Download_UMAKE
    I got this message:
    Code:
    Assembler messages:
Fatal error: can't create obj/Chromosome.o: Permission denied
In file included from GenomeSequence.h:34:0,
                 from Chromosome.h:4,
                 from Chromosome.cpp:2:
MemoryMapArray.h: In member function ‘int MemoryMapArray<elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass>::create(const char*, indexT, int)’:
MemoryMapArray.h:230:47: error: there are no arguments to ‘gethostname’ that depend on a template parameter, so a declaration of ‘gethostname’ must be available [-fpermissive]
MemoryMapArray.h:230:47: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
    Please tell me how to fix it. Thanks in advance!
    Tags: None
    • GenoMax
      Senior Member
      • Feb 2008
      • 7142
      #2
      Is that the entire error message? Are you getting that right after issuing "make" command?

      It appears that the program is unable to write to "obj" (directory).

        Comment

        • d_t_nguyen
          Member
          • Jun 2013
          • 13
          #3
          This is the entire message.
          Code:
          make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
ln  -s ../samtools/bgzf.h ../include/bgzf.h
ln  -s ../samtools/knetfile.h ../include/knetfile.h
ln  -s ../samtools/khash.h ../include/khash.h
ln  -s ../samtools/bam.h ../include/bam.h
ar -cr ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar -cr ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
ar -cr ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
ln  -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h
ln  -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h
ln  -s ../general/BaseUtilities.h ../include/BaseUtilities.h
ln  -s ../general/BasicHash.h ../include/BasicHash.h
ln  -s ../general/BgzfFileType.h ../include/BgzfFileType.h
ln  -s ../general/CharBuffer.h ../include/CharBuffer.h
ln  -s ../general/Chromosome.h ../include/Chromosome.h
ln  -s ../general/Cigar.h ../include/Cigar.h
ln  -s ../general/CigarRoller.h ../include/CigarRoller.h
ln  -s ../general/Error.h ../include/Error.h
ln  -s ../general/FastQ.h ../include/FastQ.h
ln  -s ../general/FileType.h ../include/FileType.h
ln  -s ../general/FortranFormat.h ../include/FortranFormat.h
ln  -s ../general/GenomeSequence.h ../include/GenomeSequence.h
ln  -s ../general/GenotypeLists.h ../include/GenotypeLists.h
ln  -s ../general/glfHandler.h ../include/glfHandler.h
ln  -s ../general/GzipFileType.h ../include/GzipFileType.h
ln  -s ../general/GzipHeader.h ../include/GzipHeader.h
ln  -s ../general/Hash.h ../include/Hash.h
ln  -s ../general/Input.h ../include/Input.h
ln  -s ../general/InputFile.h ../include/InputFile.h
ln  -s ../general/IntArray.h ../include/IntArray.h
ln  -s ../general/IntHash.h ../include/IntHash.h
ln  -s ../general/LongHash.h ../include/LongHash.h
ln  -s ../general/LongLongCounter.h ../include/LongLongCounter.h
ln  -s ../general/MapFunction.h ../include/MapFunction.h
ln  -s ../general/MathMatrix.h ../include/MathMatrix.h
ln  -s ../general/MathVector.h ../include/MathVector.h
ln  -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h
ln  -s ../general/MemoryInfo.h ../include/MemoryInfo.h
ln  -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h
ln  -s ../general/MemoryMap.h ../include/MemoryMap.h
ln  -s ../general/MiniDeflate.h ../include/MiniDeflate.h
ln  -s ../general/Parameters.h ../include/Parameters.h
ln  -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h
ln  -s ../general/Pedigree.h ../include/Pedigree.h
ln  -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h
ln  -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h
ln  -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h
ln  -s ../general/PedigreePerson.h ../include/PedigreePerson.h
ln  -s ../general/QuickIndex.h ../include/QuickIndex.h
ln  -s ../general/Random.h ../include/Random.h
ln  -s ../general/SmithWaterman.h ../include/SmithWaterman.h
ln  -s ../general/Sort.h ../include/Sort.h
ln  -s ../general/STLUtilities.h ../include/STLUtilities.h
ln  -s ../general/StringAlias.h ../include/StringAlias.h
ln  -s ../general/StringArray.h ../include/StringArray.h
ln  -s ../general/StringBasics.h ../include/StringBasics.h
ln  -s ../general/StringHash.h ../include/StringHash.h
ln  -s ../general/StringMap.h ../include/StringMap.h
ln  -s ../general/TrimSequence.h ../include/TrimSequence.h
ln  -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
ln  -s ../general/WindowsHelper.h ../include/WindowsHelper.h
ln  -s ../general/Constant.h ../include/Constant.h
ln  -s ../general/Generic.h ../include/Generic.h
ln  -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
ln  -s ../general/InplaceMerge.h ../include/InplaceMerge.h
ln  -s ../general/LongInt.h ../include/LongInt.h
ln  -s ../general/MathConstant.h ../include/MathConstant.h
ln  -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
ln  -s ../general/SimpleStats.h ../include/SimpleStats.h
/usr/bin/g++  -O4 -Werror -Wno-unused-variable  -Wno-unused-result -pipe -Wall -I../include -I.  -D__ZLIB_AVAILABLE__  -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"0.0.1\""
Assembler messages:
Fatal error: can't create obj/Chromosome.o: Permission denied
In file included from GenomeSequence.h:34:0,
                 from Chromosome.h:4,
                 from Chromosome.cpp:2:
MemoryMapArray.h: In member function ‘int MemoryMapArray<elementT, indexT, cookieVal, versionVal, accessorFunc, setterFunc, elementCount2BytesFunc, arrayHeaderClass>::create(const char*, indexT, int)’:
MemoryMapArray.h:230:47: error: there are no arguments to ‘gethostname’ that depend on a template parameter, so a declaration of ‘gethostname’ must be available [-fpermissive]
MemoryMapArray.h:230:47: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
make[3]: *** [obj/Chromosome.o] Error 2
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
make[1]: *** [general] Error 2
make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
make: *** [libStatGen] Error 2
          I followed exactly the instruction.

            Comment

            • GenoMax
              Senior Member
              • Feb 2008
              • 7142
              #4
              Is UMAKE_HOME variable set? Have you made the "ext" directory under UMAKE_HOME?

              What OS is this BTW?

              Note that UMAKE requires external software packages to be copied to UMAKE_HOME/ext/ directory

                Comment

                • d_t_nguyen
                  Member
                  • Jun 2013
                  • 13
                  #5
                  Yes I did. I'm using ubuntu 13.04 i386

                    Comment

                    • GenoMax
                      Senior Member
                      • Feb 2008
                      • 7142
                      #6
                      Originally posted by d_t_nguyen View Post
                      Yes I did. I'm using ubuntu 13.04 i386
                      What is UMAKE_HOME set to? /home/daithanh/Learning/1000genomes/umake?

                      Are you running 32-bit ubuntu?

                        Comment

                        • d_t_nguyen
                          Member
                          • Jun 2013
                          • 13
                          #7
                          Originally posted by GenoMax
                          UMAKE is only supported on 64-bit OS according to UMAKE page. You seem to be running 32-bit ubuntu. Is that correct?
                          Oh thank you so much! I'm so silly. I'm using 32-bit ubuntu. UMAKE seems require 64-bit os.

                            Comment

                            • GenoMax
                              Senior Member
                              • Feb 2008
                              • 7142
                              #8
                              Originally posted by d_t_nguyen View Post
                              Oh thank you so much! I'm so silly. I'm using 32-bit ubuntu. UMAKE seems require 64-bit os.
                              After I wrote that I am no longer so sure (that is what I edited my previous mesg). UMAKE page seems to indicate that development occurs both on 32-bit and 64-bit but only 64-bit processors are supported (which sounds a bit vague).

                              BTW: I am seeing the same error on 64-bit ubuntu. So let me look into this some more.

                                Comment

                                • GenoMax
                                  Senior Member
                                  • Feb 2008
                                  • 7142
                                  #9
                                  It appears that the "libStatGen" included in the UMAKE source may have a problem which is generating that error.

                                  Try the following. Go into the "umake" directory and rename "libStatGen" folder to something else (e.g. libStatGen_bak).

                                  Then get a fresh copy of libStatGen using git (as described here: http://genome.sph.umich.edu/wiki/C%2...ry:_libStatGen)
                                  Code:
                                  git clone https://github.com/statgen/libStatGen.git
                                  Go back to the top level "umake" directory and try the "make" again.
                                  Last edited by GenoMax; 06-25-2013, 05:51 AM.

                                    Comment

                                    • d_t_nguyen
                                      Member
                                      • Jun 2013
                                      • 13
                                      #10
                                      Originally posted by GenoMax View Post
                                      It appears that the "libStatGen" included in the UMAKE source may have a problem which is generating that error.

                                      Try the following. Go into the "umake" directory and rename "libStatGen" folder to something else (e.g. libStatGen_bak).

                                      Then get a fresh copy of libStatGen using git (as described here: http://genome.sph.umich.edu/wiki/C%2...ry:_libStatGen)
                                      Code:
                                      git clone https://github.com/statgen/libStatGen.git
                                      Go back to the top level "umake" directory and try the "make" again.
                                      This problem seems to be solved by this way, but i have new problem.
                                      Code:
                                      make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
ln  -s ../samtools/bgzf.h ../include/bgzf.h
ln  -s ../samtools/knetfile.h ../include/knetfile.h
ln  -s ../samtools/khash.h ../include/khash.h
ln  -s ../samtools/bam.h ../include/bam.h
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
ln  -s ../general/BaseAsciiMap.h ../include/BaseAsciiMap.h
ln  -s ../general/BaseQualityHelper.h ../include/BaseQualityHelper.h
ln  -s ../general/BaseUtilities.h ../include/BaseUtilities.h
ln  -s ../general/BasicHash.h ../include/BasicHash.h
ln  -s ../general/BgzfFileType.h ../include/BgzfFileType.h
ln  -s ../general/BgzfFileTypeRecovery.h ../include/BgzfFileTypeRecovery.h
ln  -s ../general/CharBuffer.h ../include/CharBuffer.h
ln  -s ../general/Chromosome.h ../include/Chromosome.h
ln  -s ../general/Cigar.h ../include/Cigar.h
ln  -s ../general/CigarRoller.h ../include/CigarRoller.h
ln  -s ../general/Error.h ../include/Error.h
ln  -s ../general/ErrorHandler.h ../include/ErrorHandler.h
ln  -s ../general/FileType.h ../include/FileType.h
ln  -s ../general/FortranFormat.h ../include/FortranFormat.h
ln  -s ../general/GenomeSequence.h ../include/GenomeSequence.h
ln  -s ../general/GenotypeLists.h ../include/GenotypeLists.h
ln  -s ../general/glfHandler.h ../include/glfHandler.h
ln  -s ../general/GzipFileType.h ../include/GzipFileType.h
ln  -s ../general/GzipHeader.h ../include/GzipHeader.h
ln  -s ../general/Hash.h ../include/Hash.h
ln  -s ../general/IndexBase.h ../include/IndexBase.h
ln  -s ../general/Input.h ../include/Input.h
ln  -s ../general/InputFile.h ../include/InputFile.h
ln  -s ../general/IntArray.h ../include/IntArray.h
ln  -s ../general/IntHash.h ../include/IntHash.h
ln  -s ../general/LongLongCounter.h ../include/LongLongCounter.h
ln  -s ../general/MapFunction.h ../include/MapFunction.h
ln  -s ../general/MathMatrix.h ../include/MathMatrix.h
ln  -s ../general/MathVector.h ../include/MathVector.h
ln  -s ../general/MemoryAllocators.h ../include/MemoryAllocators.h
ln  -s ../general/MemoryInfo.h ../include/MemoryInfo.h
ln  -s ../general/MemoryMapArray.h ../include/MemoryMapArray.h
ln  -s ../general/MemoryMap.h ../include/MemoryMap.h
ln  -s ../general/MiniDeflate.h ../include/MiniDeflate.h
ln  -s ../general/NonOverlapRegions.h ../include/NonOverlapRegions.h
ln  -s ../general/Parameters.h ../include/Parameters.h
ln  -s ../general/PedigreeAlleleFreq.h ../include/PedigreeAlleleFreq.h
ln  -s ../general/Pedigree.h ../include/Pedigree.h
ln  -s ../general/PedigreeDescription.h ../include/PedigreeDescription.h
ln  -s ../general/PedigreeFamily.h ../include/PedigreeFamily.h
ln  -s ../general/PedigreeGlobals.h ../include/PedigreeGlobals.h
ln  -s ../general/PedigreePerson.h ../include/PedigreePerson.h
ln  -s ../general/QuickIndex.h ../include/QuickIndex.h
ln  -s ../general/Random.h ../include/Random.h
ln  -s ../general/ReferenceSequence.h ../include/ReferenceSequence.h
ln  -s ../general/SmithWaterman.h ../include/SmithWaterman.h
ln  -s ../general/Sort.h ../include/Sort.h
ln  -s ../general/STLUtilities.h ../include/STLUtilities.h
ln  -s ../general/StatGenStatus.h ../include/StatGenStatus.h
ln  -s ../general/StringAlias.h ../include/StringAlias.h
ln  -s ../general/StringArray.h ../include/StringArray.h
ln  -s ../general/StringBasics.h ../include/StringBasics.h
ln  -s ../general/StringHash.h ../include/StringHash.h
ln  -s ../general/StringMap.h ../include/StringMap.h
ln  -s ../general/Tabix.h ../include/Tabix.h
ln  -s ../general/UncompressedFileType.h ../include/UncompressedFileType.h
ln  -s ../general/WindowsHelper.h ../include/WindowsHelper.h
ln  -s ../general/Constant.h ../include/Constant.h
ln  -s ../general/CSG_MD5.h ../include/CSG_MD5.h
ln  -s ../general/Generic.h ../include/Generic.h
ln  -s ../general/GenomeSequenceHelpers.h ../include/GenomeSequenceHelpers.h
ln  -s ../general/GreedyTupleAligner.h ../include/GreedyTupleAligner.h
ln  -s ../general/InplaceMerge.h ../include/InplaceMerge.h
ln  -s ../general/LongHash.h ../include/LongHash.h
ln  -s ../general/LongInt.h ../include/LongInt.h
ln  -s ../general/MathConstant.h ../include/MathConstant.h
ln  -s ../general/PackedVector.h ../include/PackedVector.h
ln  -s ../general/PedigreeAlleles.h ../include/PedigreeAlleles.h
ln  -s ../general/Performance.h ../include/Performance.h
ln  -s ../general/ReusableVector.h ../include/ReusableVector.h
ln  -s ../general/SimpleStats.h ../include/SimpleStats.h
ln  -s ../general/TrimSequence.h ../include/TrimSequence.h
ln  -s ../general/UnitTest.h ../include/UnitTest.h
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
ln  -s ../bam/SamFileHeader.h ../include/SamFileHeader.h
ln  -s ../bam/SamFile.h ../include/SamFile.h
ln  -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h
ln  -s ../bam/SamInterface.h ../include/SamInterface.h
ln  -s ../bam/BamInterface.h ../include/BamInterface.h
ln  -s ../bam/SamRecord.h ../include/SamRecord.h
ln  -s ../bam/BamIndex.h ../include/BamIndex.h
ln  -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h
ln  -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h
ln  -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h
ln  -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h
ln  -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h
ln  -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h
ln  -s ../bam/SamValidation.h ../include/SamValidation.h
ln  -s ../bam/SamStatistics.h ../include/SamStatistics.h
ln  -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h
ln  -s ../bam/SamFilter.h ../include/SamFilter.h
ln  -s ../bam/PileupElement.h ../include/PileupElement.h
ln  -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h
ln  -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h
ln  -s ../bam/SamTags.h ../include/SamTags.h
ln  -s ../bam/PosList.h ../include/PosList.h
ln  -s ../bam/CigarHelper.h ../include/CigarHelper.h
ln  -s ../bam/SamRecordPool.h ../include/SamRecordPool.h
ln  -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h
ln  -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h
ln  -s ../bam/Pileup.h ../include/Pileup.h
ln  -s ../bam/SamHelper.h ../include/SamHelper.h
ln  -s ../bam/SamFlag.h ../include/SamFlag.h
ln  -s ../bam/SamStatus.h ../include/SamStatus.h
ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
ln  -s ../fastq/FastQFile.h ../include/FastQFile.h
ln  -s ../fastq/BaseCount.h ../include/BaseCount.h
ln  -s ../fastq/BaseComposition.h ../include/BaseComposition.h
ln  -s ../fastq/FastQStatus.h ../include/FastQStatus.h
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
ln  -s ../glf/GlfException.h ../include/GlfException.h
ln  -s ../glf/GlfFile.h ../include/GlfFile.h
ln  -s ../glf/GlfHeader.h ../include/GlfHeader.h
ln  -s ../glf/GlfRecord.h ../include/GlfRecord.h
ln  -s ../glf/GlfRefSection.h ../include/GlfRefSection.h
ln  -s ../glf/GlfStatus.h ../include/GlfStatus.h
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
ln  -s ../vcf/VcfFile.h ../include/VcfFile.h
ln  -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h
ln  -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h
ln  -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h
ln  -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h
ln  -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h
ln  -s ../vcf/VcfHeader.h ../include/VcfHeader.h
ln  -s ../vcf/VcfHelper.h ../include/VcfHelper.h
ln  -s ../vcf/VcfRecord.h ../include/VcfRecord.h
ln  -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h
ln  -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h
ln  -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h
ln  -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h
ln  -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h
ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
mkdir --p lib/
cd lib/; ln -s ../libStatGen/libStatGen.a libStatGen.a; cd ..
make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
make[1]: *** No rule to make target `opt'.  Stop.
make: *** [samtools-hybrid] Error 2
                                      Do you have any suggestion?
                                      Last edited by d_t_nguyen; 06-25-2013, 07:02 AM.

                                        Comment

                                        • GenoMax
                                          Senior Member
                                          • Feb 2008
                                          • 7142
                                          #11
                                          Can you try the following?

                                          Code:
                                          make all

                                            Comment

                                            • d_t_nguyen
                                              Member
                                              • Jun 2013
                                              • 13
                                              #12
                                              Originally posted by GenoMax View Post
                                              Can you try the following?

                                              Code:
                                              make all
                                              I tried and got this message:
                                              Code:
                                              make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
ar -cru ../libStatGen_debug.a obj/debug/bgzf.o obj/debug/knetfile.o
ar -cru ../libStatGen_profile.a obj/profile/bgzf.o obj/profile/knetfile.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/samtools'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/ErrorHandler.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/IndexBase.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StatGenStatus.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/Tabix.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
mkdir -p obj/debug
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/BaseAsciiMap.o obj/debug/BaseQualityHelper.o obj/debug/BaseUtilities.o obj/debug/BasicHash.o obj/debug/BgzfFileType.o obj/debug/BgzfFileTypeRecovery.o obj/debug/CharBuffer.o obj/debug/Chromosome.o obj/debug/Cigar.o obj/debug/CigarRoller.o obj/debug/Error.o obj/debug/ErrorHandler.o obj/debug/FileType.o obj/debug/FortranFormat.o obj/debug/GenomeSequence.o obj/debug/GenotypeLists.o obj/debug/glfHandler.o obj/debug/GzipFileType.o obj/debug/GzipHeader.o obj/debug/Hash.o obj/debug/IndexBase.o obj/debug/Input.o obj/debug/InputFile.o obj/debug/IntArray.o obj/debug/IntHash.o obj/debug/LongLongCounter.o obj/debug/MapFunction.o obj/debug/MathMatrix.o obj/debug/MathVector.o obj/debug/MemoryAllocators.o obj/debug/MemoryInfo.o obj/debug/MemoryMapArray.o obj/debug/MemoryMap.o obj/debug/MiniDeflate.o obj/debug/NonOverlapRegions.o obj/debug/Parameters.o obj/debug/PedigreeAlleleFreq.o obj/debug/Pedigree.o obj/debug/PedigreeDescription.o obj/debug/PedigreeFamily.o obj/debug/PedigreeGlobals.o obj/debug/PedigreePerson.o obj/debug/QuickIndex.o obj/debug/Random.o obj/debug/ReferenceSequence.o obj/debug/SmithWaterman.o obj/debug/Sort.o obj/debug/STLUtilities.o obj/debug/StatGenStatus.o obj/debug/StringAlias.o obj/debug/StringArray.o obj/debug/StringBasics.o obj/debug/StringHash.o obj/debug/StringMap.o obj/debug/Tabix.o obj/debug/UncompressedFileType.o obj/debug/WindowsHelper.o obj/debug/PedigreeLoader.o obj/debug/PedigreeTrim.o obj/debug/PedigreeTwin.o
mkdir -p obj/profile
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseAsciiMap.o -c BaseAsciiMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseQualityHelper.o -c BaseQualityHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseUtilities.o -c BaseUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BasicHash.o -c BasicHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BgzfFileType.o -c BgzfFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BgzfFileTypeRecovery.o -c BgzfFileTypeRecovery.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CharBuffer.o -c CharBuffer.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Chromosome.o -c Chromosome.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Cigar.o -c Cigar.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CigarRoller.o -c CigarRoller.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Error.o -c Error.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/ErrorHandler.o -c ErrorHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FileType.o -c FileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FortranFormat.o -c FortranFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenomeSequence.o -c GenomeSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenotypeLists.o -c GenotypeLists.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/glfHandler.o -c glfHandler.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GzipFileType.o -c GzipFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GzipHeader.o -c GzipHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Hash.o -c Hash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IndexBase.o -c IndexBase.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Input.o -c Input.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/InputFile.o -c InputFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IntArray.o -c IntArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/IntHash.o -c IntHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/LongLongCounter.o -c LongLongCounter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MapFunction.o -c MapFunction.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MathMatrix.o -c MathMatrix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MathVector.o -c MathVector.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryAllocators.o -c MemoryAllocators.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryInfo.o -c MemoryInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryMapArray.o -c MemoryMapArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MemoryMap.o -c MemoryMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/MiniDeflate.o -c MiniDeflate.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/NonOverlapRegions.o -c NonOverlapRegions.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Parameters.o -c Parameters.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeAlleleFreq.o -c PedigreeAlleleFreq.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Pedigree.o -c Pedigree.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeDescription.o -c PedigreeDescription.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeFamily.o -c PedigreeFamily.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeGlobals.o -c PedigreeGlobals.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreePerson.o -c PedigreePerson.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/QuickIndex.o -c QuickIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Random.o -c Random.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/ReferenceSequence.o -c ReferenceSequence.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SmithWaterman.o -c SmithWaterman.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Sort.o -c Sort.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/STLUtilities.o -c STLUtilities.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StatGenStatus.o -c StatGenStatus.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringAlias.o -c StringAlias.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringArray.o -c StringArray.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/WindowsHelper.o -c WindowsHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall -Werror -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_profile.a obj/profile/BaseAsciiMap.o obj/profile/BaseQualityHelper.o obj/profile/BaseUtilities.o obj/profile/BasicHash.o obj/profile/BgzfFileType.o obj/profile/BgzfFileTypeRecovery.o obj/profile/CharBuffer.o obj/profile/Chromosome.o obj/profile/Cigar.o obj/profile/CigarRoller.o obj/profile/Error.o obj/profile/ErrorHandler.o obj/profile/FileType.o obj/profile/FortranFormat.o obj/profile/GenomeSequence.o obj/profile/GenotypeLists.o obj/profile/glfHandler.o obj/profile/GzipFileType.o obj/profile/GzipHeader.o obj/profile/Hash.o obj/profile/IndexBase.o obj/profile/Input.o obj/profile/InputFile.o obj/profile/IntArray.o obj/profile/IntHash.o obj/profile/LongLongCounter.o obj/profile/MapFunction.o obj/profile/MathMatrix.o obj/profile/MathVector.o obj/profile/MemoryAllocators.o obj/profile/MemoryInfo.o obj/profile/MemoryMapArray.o obj/profile/MemoryMap.o obj/profile/MiniDeflate.o obj/profile/NonOverlapRegions.o obj/profile/Parameters.o obj/profile/PedigreeAlleleFreq.o obj/profile/Pedigree.o obj/profile/PedigreeDescription.o obj/profile/PedigreeFamily.o obj/profile/PedigreeGlobals.o obj/profile/PedigreePerson.o obj/profile/QuickIndex.o obj/profile/Random.o obj/profile/ReferenceSequence.o obj/profile/SmithWaterman.o obj/profile/Sort.o obj/profile/STLUtilities.o obj/profile/StatGenStatus.o obj/profile/StringAlias.o obj/profile/StringArray.o obj/profile/StringBasics.o obj/profile/StringHash.o obj/profile/StringMap.o obj/profile/Tabix.o obj/profile/UncompressedFileType.o obj/profile/WindowsHelper.o obj/profile/PedigreeLoader.o obj/profile/PedigreeTrim.o obj/profile/PedigreeTwin.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/general'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
ln  -s ../bam/SamFileHeader.h ../include/SamFileHeader.h
ln  -s ../bam/SamFile.h ../include/SamFile.h
ln  -s ../bam/GenericSamInterface.h ../include/GenericSamInterface.h
ln  -s ../bam/SamInterface.h ../include/SamInterface.h
ln  -s ../bam/BamInterface.h ../include/BamInterface.h
ln  -s ../bam/SamRecord.h ../include/SamRecord.h
ln  -s ../bam/BamIndex.h ../include/BamIndex.h
ln  -s ../bam/SamHeaderHD.h ../include/SamHeaderHD.h
ln  -s ../bam/SamHeaderPG.h ../include/SamHeaderPG.h
ln  -s ../bam/SamHeaderRecord.h ../include/SamHeaderRecord.h
ln  -s ../bam/SamHeaderSQ.h ../include/SamHeaderSQ.h
ln  -s ../bam/SamHeaderRG.h ../include/SamHeaderRG.h
ln  -s ../bam/SamHeaderTag.h ../include/SamHeaderTag.h
ln  -s ../bam/SamValidation.h ../include/SamValidation.h
ln  -s ../bam/SamStatistics.h ../include/SamStatistics.h
ln  -s ../bam/SamQuerySeqWithRefHelper.h ../include/SamQuerySeqWithRefHelper.h
ln  -s ../bam/SamFilter.h ../include/SamFilter.h
ln  -s ../bam/PileupElement.h ../include/PileupElement.h
ln  -s ../bam/PileupElementBaseQual.h ../include/PileupElementBaseQual.h
ln  -s ../bam/SamReferenceInfo.h ../include/SamReferenceInfo.h
ln  -s ../bam/SamTags.h ../include/SamTags.h
ln  -s ../bam/PosList.h ../include/PosList.h
ln  -s ../bam/CigarHelper.h ../include/CigarHelper.h
ln  -s ../bam/SamRecordPool.h ../include/SamRecordPool.h
ln  -s ../bam/SamCoordOutput.h ../include/SamCoordOutput.h
ln  -s ../bam/SamRecordHelper.h ../include/SamRecordHelper.h
ln  -s ../bam/Pileup.h ../include/Pileup.h
ln  -s ../bam/SamHelper.h ../include/SamHelper.h
ln  -s ../bam/SamFlag.h ../include/SamFlag.h
ln  -s ../bam/SamStatus.h ../include/SamStatus.h
mkdir -p obj
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
mkdir -p obj/debug
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/SamFileHeader.o obj/debug/SamFile.o obj/debug/GenericSamInterface.o obj/debug/SamInterface.o obj/debug/BamInterface.o obj/debug/SamRecord.o obj/debug/BamIndex.o obj/debug/SamHeaderHD.o obj/debug/SamHeaderPG.o obj/debug/SamHeaderRecord.o obj/debug/SamHeaderSQ.o obj/debug/SamHeaderRG.o obj/debug/SamHeaderTag.o obj/debug/SamValidation.o obj/debug/SamStatistics.o obj/debug/SamQuerySeqWithRefHelper.o obj/debug/SamFilter.o obj/debug/PileupElement.o obj/debug/PileupElementBaseQual.o obj/debug/SamReferenceInfo.o obj/debug/SamTags.o obj/debug/PosList.o obj/debug/CigarHelper.o obj/debug/SamRecordPool.o obj/debug/SamCoordOutput.o obj/debug/SamRecordHelper.o
mkdir -p obj/profile
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_profile.a obj/profile/SamFileHeader.o obj/profile/SamFile.o obj/profile/GenericSamInterface.o obj/profile/SamInterface.o obj/profile/BamInterface.o obj/profile/SamRecord.o obj/profile/BamIndex.o obj/profile/SamHeaderHD.o obj/profile/SamHeaderPG.o obj/profile/SamHeaderRecord.o obj/profile/SamHeaderSQ.o obj/profile/SamHeaderRG.o obj/profile/SamHeaderTag.o obj/profile/SamValidation.o obj/profile/SamStatistics.o obj/profile/SamQuerySeqWithRefHelper.o obj/profile/SamFilter.o obj/profile/PileupElement.o obj/profile/PileupElementBaseQual.o obj/profile/SamReferenceInfo.o obj/profile/SamTags.o obj/profile/PosList.o obj/profile/CigarHelper.o obj/profile/SamRecordPool.o obj/profile/SamCoordOutput.o obj/profile/SamRecordHelper.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/bam'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
ln  -s ../fastq/FastQFile.h ../include/FastQFile.h
ln  -s ../fastq/BaseCount.h ../include/BaseCount.h
ln  -s ../fastq/BaseComposition.h ../include/BaseComposition.h
ln  -s ../fastq/FastQStatus.h ../include/FastQStatus.h
mkdir -p obj
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
mkdir -p obj/debug
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/FastQFile.o obj/debug/BaseCount.o obj/debug/BaseComposition.o obj/debug/FastQStatus.o
mkdir -p obj/profile
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_profile.a obj/profile/FastQFile.o obj/profile/BaseCount.o obj/profile/BaseComposition.o obj/profile/FastQStatus.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/fastq'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
ln  -s ../glf/GlfException.h ../include/GlfException.h
ln  -s ../glf/GlfFile.h ../include/GlfFile.h
ln  -s ../glf/GlfHeader.h ../include/GlfHeader.h
ln  -s ../glf/GlfRecord.h ../include/GlfRecord.h
ln  -s ../glf/GlfRefSection.h ../include/GlfRefSection.h
ln  -s ../glf/GlfStatus.h ../include/GlfStatus.h
mkdir -p obj
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
mkdir -p obj/debug
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/GlfException.o obj/debug/GlfFile.o obj/debug/GlfHeader.o obj/debug/GlfRecord.o obj/debug/GlfRefSection.o obj/debug/GlfStatus.o
mkdir -p obj/profile
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfException.o -c GlfException.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfFile.o -c GlfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfHeader.o -c GlfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfRecord.o -c GlfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfRefSection.o -c GlfRefSection.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/GlfStatus.o -c GlfStatus.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_profile.a obj/profile/GlfException.o obj/profile/GlfFile.o obj/profile/GlfHeader.o obj/profile/GlfRecord.o obj/profile/GlfRefSection.o obj/profile/GlfStatus.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/glf'
make[2]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
ln  -s ../vcf/VcfFile.h ../include/VcfFile.h
ln  -s ../vcf/VcfFileReader.h ../include/VcfFileReader.h
ln  -s ../vcf/VcfFileWriter.h ../include/VcfFileWriter.h
ln  -s ../vcf/VcfGenotypeField.h ../include/VcfGenotypeField.h
ln  -s ../vcf/VcfGenotypeFormat.h ../include/VcfGenotypeFormat.h
ln  -s ../vcf/VcfGenotypeSample.h ../include/VcfGenotypeSample.h
ln  -s ../vcf/VcfHeader.h ../include/VcfHeader.h
ln  -s ../vcf/VcfHelper.h ../include/VcfHelper.h
ln  -s ../vcf/VcfRecord.h ../include/VcfRecord.h
ln  -s ../vcf/VcfRecordField.h ../include/VcfRecordField.h
ln  -s ../vcf/VcfRecordFilter.h ../include/VcfRecordFilter.h
ln  -s ../vcf/VcfRecordGenotype.h ../include/VcfRecordGenotype.h
ln  -s ../vcf/VcfRecordInfo.h ../include/VcfRecordInfo.h
ln  -s ../vcf/VcfSubsetSamples.h ../include/VcfSubsetSamples.h
mkdir -p obj
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen.a obj/VcfFile.o obj/VcfFileReader.o obj/VcfFileWriter.o obj/VcfGenotypeField.o obj/VcfGenotypeFormat.o obj/VcfGenotypeSample.o obj/VcfHeader.o obj/VcfHelper.o obj/VcfRecord.o obj/VcfRecordField.o obj/VcfRecordFilter.o obj/VcfRecordGenotype.o obj/VcfRecordInfo.o obj/VcfSubsetSamples.o
mkdir -p obj/debug
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/debug/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_debug.a obj/debug/VcfFile.o obj/debug/VcfFileReader.o obj/debug/VcfFileWriter.o obj/debug/VcfGenotypeField.o obj/debug/VcfGenotypeFormat.o obj/debug/VcfGenotypeSample.o obj/debug/VcfHeader.o obj/debug/VcfHelper.o obj/debug/VcfRecord.o obj/debug/VcfRecordField.o obj/debug/VcfRecordFilter.o obj/debug/VcfRecordGenotype.o obj/debug/VcfRecordInfo.o obj/debug/VcfSubsetSamples.o
mkdir -p obj/profile
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
g++   -pipe -Wall  -I../include -I.  -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/profile/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
ar -cru ../libStatGen_profile.a obj/profile/VcfFile.o obj/profile/VcfFileReader.o obj/profile/VcfFileWriter.o obj/profile/VcfGenotypeField.o obj/profile/VcfGenotypeFormat.o obj/profile/VcfGenotypeSample.o obj/profile/VcfHeader.o obj/profile/VcfHelper.o obj/profile/VcfRecord.o obj/profile/VcfRecordField.o obj/profile/VcfRecordFilter.o obj/profile/VcfRecordGenotype.o obj/profile/VcfRecordInfo.o obj/profile/VcfSubsetSamples.o
make[2]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen/vcf'
make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/libStatGen'
mkdir --p lib/
cd lib/; ln -s ../libStatGen/libStatGen.a libStatGen.a; cd ..
make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bgzf.c -o bgzf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  kstring.c -o kstring.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam.c -o bam.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_import.c -o bam_import.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  sam.c -o sam.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_index.c -o bam_index.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_pileup.c -o bam_pileup.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_md.c -o bam_md.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  glf.c -o glf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  razf.c -o razf.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  faidx.c -o faidx.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  knetfile.c -o knetfile.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  sam_header.c -o sam_header.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  kprobaln.c -o kprobaln.o
ar -cru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o glf.o razf.o faidx.o knetfile.o bam_sort.o sam_header.o kprobaln.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_tview.c -o bam_tview.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_maqcns.c -o bam_maqcns.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  sam_view.c -o sam_view.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_stat.c -o bam_stat.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bam_color.c -o bam_color.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  bamtk.c -o bamtk.o
gcc -c -g -Wall -O2  -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1  kaln.c -o kaln.o
mkdir --p bin/
gcc -g -Wall -O2  -o bin/samtools-hybrid bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o -lm  -lcurses  -lz -L. -lbam
make[1]: Leaving directory `/home/daithanh/Learning/1000genomes/umake/samtools-hybrid'
bgzf.c: In function ‘bgzf_close’:
bgzf.c:587:8: warning: variable ‘count’ set but not used [-Wunused-but-set-variable]
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:276:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:283:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:296:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:299:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:303:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:307:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:317:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
bam_index.c:321:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_close’:
razf.c:804:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:805:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:808:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:810:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_end_flush’:
razf.c:258:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘_razf_write’:
razf.c:201:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘save_zindex’:
razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_flush’:
razf.c:221:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
razf.c:234:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:416:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:237:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
kprobaln.c: In function ‘kpa_glocal’:
kprobaln.c:78:21: warning: variable ‘is_diff’ set but not used [-Wunused-but-set-variable]
./libbam.a(bgzf.o): In function `deflate_block':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:272: undefined reference to `deflate'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:274: undefined reference to `deflateEnd'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:266: undefined reference to `deflateInit2_'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:290: undefined reference to `deflateEnd'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:306: undefined reference to `crc32'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:307: undefined reference to `crc32'
./libbam.a(bgzf.o): In function `inflate_block':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:340: undefined reference to `inflateInit2_'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:345: undefined reference to `inflate'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:351: undefined reference to `inflateEnd'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bgzf.c:347: undefined reference to `inflateEnd'
./libbam.a(bam_import.o): In function `ks_getuntil':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:17: undefined reference to `gzread'
./libbam.a(bam_import.o): In function `__bam_get_lines':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:76: undefined reference to `gzdopen'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:92: undefined reference to `gzclose'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:76: undefined reference to `gzopen64'
./libbam.a(bam_import.o): In function `sam_header_read2':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:126: undefined reference to `gzdopen'
./libbam.a(bam_import.o): In function `ks_getc':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:17: undefined reference to `gzread'
./libbam.a(bam_import.o): In function `sam_header_read2':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:143: undefined reference to `gzclose'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:126: undefined reference to `gzopen64'
./libbam.a(bam_import.o): In function `sam_open':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:422: undefined reference to `gzdopen'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:422: undefined reference to `gzopen64'
./libbam.a(bam_import.o): In function `sam_close':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/bam_import.c:435: undefined reference to `gzclose'
./libbam.a(razf.o): In function `_razf_write':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:197: undefined reference to `deflate'
./libbam.a(razf.o): In function `razf_open_w':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:170: undefined reference to `deflateInit2_'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:186: undefined reference to `deflateSetHeader'
./libbam.a(razf.o): In function `razf_open_r':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:389: undefined reference to `inflateInit2_'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:390: undefined reference to `inflateEnd'
./libbam.a(razf.o): In function `_razf_read':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:602: undefined reference to `inflate'
./libbam.a(razf.o): In function `razf_flush':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:230: undefined reference to `deflate'
./libbam.a(razf.o): In function `_razf_reset_read':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:709: undefined reference to `inflateReset'
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:709: undefined reference to `inflateReset'
./libbam.a(razf.o): In function `razf_close':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:826: undefined reference to `inflateEnd'
./libbam.a(razf.o): In function `razf_end_flush':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:254: undefined reference to `deflate'
./libbam.a(razf.o): In function `razf_close':
/home/daithanh/Learning/1000genomes/umake/samtools-hybrid/razf.c:800: undefined reference to `deflateEnd'
collect2: error: ld returned 1 exit status
make[1]: *** [bin/samtools-hybrid] Error 1
make: *** [samtools-hybrid] Error 2

                                                Comment

                                                • GenoMax
                                                  Senior Member
                                                  • Feb 2008
                                                  • 7142
                                                  #13
                                                  Do the following:

                                                  Code:
                                                  cd samtools-hybrid
cp Makefile Makefile.orig
                                                  Open the Makefile with an editor of your choice. Find the line

                                                  Code:
                                                  $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) [COLOR="Red"]-lz[/COLOR] -L. -lbam
                                                  Change it by moving -lz to the end of the line and save the file

                                                  Code:
                                                  $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam [COLOR="Red"]-lz[/COLOR]
                                                  Try
                                                  Code:
                                                  make all
                                                  again from the main umake directory.

                                                    Comment

                                                    • d_t_nguyen
                                                      Member
                                                      • Jun 2013
                                                      • 13
                                                      #14
                                                      This is the message, I have to paste it to pastebin because the forum does not allow too long post.
                                                      make[1]: Entering directory `/home/daithanh/Learning/1000genomes/umake/libStatGe - Pastebin.com
                                                      http://pastebin.com/g5rvhfQx
                                                      Pastebin.com is the number one paste tool since 2002. Pastebin is a website where you can store text online for a set period of time.

                                                        Comment

                                                        • GenoMax
                                                          Senior Member
                                                          • Feb 2008
                                                          • 7142
                                                          #15
                                                          Looks like you are going to have to contact the UMAKE authors to see if they can help. I can't get the glf* tools to compile either.

                                                            Comment

                                                            Previous 1 2 template Next

                                                            Latest Articles

                                                            Collapse
                                                            • SEQadmin2
                                                              Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
                                                              by SEQadmin2



                                                              CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

                                                              Despite this, “CRISPR helped turn genome editing from a specialized technique into                                                              ...
                                                              07-31-2026, 11:01 AM
                                                            • SEQadmin2
                                                              Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
                                                              by SEQadmin2


                                                              Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

                                                              The systematic characterization of the human proteome has                                                              ...
                                                              07-20-2026, 11:48 AM
                                                            View All

                                                            ad_right_rmr

                                                            Collapse

                                                            News

                                                            Collapse
                                                            Topics Statistics Last Post
                                                            Single-Cell Atlas Pinpoints Spinal Neurons Controlling Movement Speed by SEQadmin2
                                                            Started by SEQadmin2, Yesterday, 10:35 AM
                                                            0 responses
                                                            7 views
                                                            0 reactions
                                                            		 Last Post SEQadmin2
                                                            by SEQadmin2
                                                            Yesterday, 10:35 AM  
                                                            Consortium Completes First Full Diploid Human Genome by SEQadmin2
                                                            Started by SEQadmin2, 08-06-2026, 07:41 AM
                                                            0 responses
                                                            26 views
                                                            0 reactions
                                                            		 Last Post SEQadmin2
                                                            by SEQadmin2
                                                            08-06-2026, 07:41 AM  
                                                            Long-Read Sequencing Closes Decades-Old Gaps in the Medaka Genome by SEQadmin2
                                                            Started by SEQadmin2, 08-03-2026, 10:13 AM
                                                            0 responses
                                                            45 views
                                                            0 reactions
                                                            		 Last Post SEQadmin2
                                                            by SEQadmin2
                                                            08-03-2026, 10:13 AM  
                                                            New Genomic Method Uncovers Ancient Hominin DNA by SEQadmin2
                                                            Started by SEQadmin2, 07-31-2026, 02:55 AM
                                                            0 responses
                                                            48 views
                                                            0 reactions
                                                            		 Last Post SEQadmin2
                                                            by SEQadmin2
                                                            07-31-2026, 02:55 AM  
                                                            View All
                                                            Working...