PileLine 1.1 has been released !!
PileLine 1.1 at http://sing.ei.uvigo.es/pileline/index.php/Main_Page
The major changes in this version are:
-New pileline-fulljoin command to join n GP files.
-New pileline-nsmc mode: intervals mode. Now it can check the reproducibility of mutations by entire intervals (i.e.:genes, provided as .bed), instead of only exact genome position.
-Added BGZF compatibility. This is the samtools compressed format of GP files. All PileLine commands are adapted to receive both bgz-compressed or uncompressed files, transparently. If you want to know how to compress your GP files, please see: tabix.
-Added .fai compatibility for genome indexes (needed in pileline-genotest). The pileline-genindex command is now deprecated. You should use the "samtools faidx" command instead.
-Added more flexibility to include custom GP files, by indicating the sequence, start and stop columns in files.
-Bugfix: Bed files is treated in the standard form: (0-based and the last position in the interval is excluded).
-Bugfix: Prevent fastseek from hanging due to bad input files (i.e.: zip compressed, non-ascii, non tab-separated). A small heuristic check is included before processing the file.
The major changes in this version are:
-New pileline-fulljoin command to join n GP files.
-New pileline-nsmc mode: intervals mode. Now it can check the reproducibility of mutations by entire intervals (i.e.:genes, provided as .bed), instead of only exact genome position.
-Added BGZF compatibility. This is the samtools compressed format of GP files. All PileLine commands are adapted to receive both bgz-compressed or uncompressed files, transparently. If you want to know how to compress your GP files, please see: tabix.
-Added .fai compatibility for genome indexes (needed in pileline-genotest). The pileline-genindex command is now deprecated. You should use the "samtools faidx" command instead.
-Added more flexibility to include custom GP files, by indicating the sequence, start and stop columns in files.
-Bugfix: Bed files is treated in the standard form: (0-based and the last position in the interval is excluded).
-Bugfix: Prevent fastseek from hanging due to bad input files (i.e.: zip compressed, non-ascii, non tab-separated). A small heuristic check is included before processing the file.