[jjcook]

Place this near the top of param.cpp:

#include<stdlib.h>

[ECO]

No luck...I'm corresponding with the SOAP team, hopefully they will be able to help me through it. Thanks for the help jjcook

g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c param.cpp -o param.chr.o
g++ -DMAXGAP=3 -DMAXHITS=10000 -DTHREAD -O3   -DDB_CHR -DREAD_60  -c reads.cpp -o reads.chr.o
reads.cpp: In member function ‘void ReadClass::CheckFile(std::ifstream&)’:
reads.cpp:32: error: ‘exit’ was not declared in this scope
reads.cpp:37: error: ‘exit’ was not declared in this scope
reads.cpp:41: error: ‘exit’ was not declared in this scope
make: *** [reads.chr.o] Error 1

[ECO]

New version out today... see:

ftp://ftp.genomics.org.cn/pub/soap/

[ECO]

1.11 has solved all my compiling problems. Now to find some indels!

[bioinfosm]

Any luck with soap on indels?
I tried it on my paired-end data, but soapsnp ends up in segmentation fault!
I think I did fine on the sort (confused about sorting a paired end alignment on coordinates!) .. does soap not use the information of pairs after mapping them!

[allo]

Hi, more SOAP,
The SOAP2 paper states that the new SOAP2 supports several input and output formats:
The output formats include a SOAP tab-delimited
text table, a gzipped text table, a Sequence Alignment/Map (SAM)
format and its binary equivalent (BAM) that is recommended by
the 1000 Genomes Consortium, and a Consed format that fits with
the assembly viewer.
Does anybody know how to select those formats? I have not been able to find any info on the documentation or web site.
Thanks!!

[allo]

By the way this is the link to SOAP2 version 2.19

http://soap.genomics.org.cn/soapaligner.html

Cheers!

[amaer]

Does SOAP2 perform gapped alignments yet?