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Place this near the top of param.cpp:
Code:
#include<stdlib.h>
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No luck...I'm corresponding with the SOAP team, hopefully they will be able to help me through it. Thanks for the help jjcook
Code: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
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1.11 has solved all my compiling problems. Now to find some indels!
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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!--
bioinfosmComment
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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!!Comment
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By the way this is the link to SOAP2 version 2.19
Cheers!Comment
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Does SOAP2 perform gapped alignments yet?Comment
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