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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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