Parse CIGAR string in C/C++

tedwong · 03-19-2015, 05:49 PM

What'd be the best way to parse a CIGAR string fully according to the specification in C/C++? Would regular expression work?

Brian Bushnell · 03-19-2015, 09:15 PM

Quote:

Originally Posted by tedwong

What'd be the best way to parse a CIGAR string fully according to the specification in C/C++? Would regular expression work?

No. Unless you simply want to detect the presence of some operation, the best way is with a custom loop.

Here's an example in Java that can easily be translated to C++:

http://seqanswers.com/forums/showthread.php?t=51162

dpryan · 03-20-2015, 01:31 AM

If you're using C/C++ already, then just use htslib. The functions for this have already been written (afterall, it's what samtools uses) and the API is generally convenient.

lindenb · 03-20-2015, 02:29 AM

cross posted: http://stackoverflow.com/questions/2...lar-expression

student-t · 04-08-2015, 04:30 AM

For reference (using the htslib library)

#include <htslib/sam.h>

auto f = sam_open(file.c_str(), "r");
auto h = sam_hdr_read(f);
auto t = bam_init1();

while (sam_read1(f, h, t) >= 0)
{
auto id = std::string(h->target_name[0]);
auto mapped = !(t->core.flag & BAM_FUNMAP);

const auto cigar = bam_get_cigar(t);

for (int k = 0; k < t->core.n_cigar; k++)
{
const int op = bam_cigar_op(cigar[k]);
const int ol = bam_cigar_oplen(cigar[k]);

if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CDEL)
{
// your code, you have the length in ol (eg: 101M -> ol == 101)
}
}
}

sam_close(f);

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03-19-2015, 05:49 PM	#1
tedwong Member Location: Sydney Join Date: Mar 2015 Posts: 13	Parse CIGAR string in C/C++ What'd be the best way to parse a CIGAR string fully according to the specification in C/C++? Would regular expression work?

03-20-2015, 01:31 AM	#3
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	If you're using C/C++ already, then just use htslib. The functions for this have already been written (afterall, it's what samtools uses) and the API is generally convenient.

03-20-2015, 02:29 AM	#4
lindenb Senior Member Location: France Join Date: Apr 2010 Posts: 143	cross posted: http://stackoverflow.com/questions/2...lar-expression

04-08-2015, 04:30 AM	#5
student-t Member Location: Garvan Institute Join Date: Mar 2015 Posts: 16	For reference (using the htslib library) #include <htslib/sam.h> auto f = sam_open(file.c_str(), "r"); auto h = sam_hdr_read(f); auto t = bam_init1(); while (sam_read1(f, h, t) >= 0) { auto id = std::string(h->target_name[0]); auto mapped = !(t->core.flag & BAM_FUNMAP); const auto cigar = bam_get_cigar(t); for (int k = 0; k < t->core.n_cigar; k++) { const int op = bam_cigar_op(cigar[k]); const int ol = bam_cigar_oplen(cigar[k]); if (op == BAM_CMATCH \|\| op == BAM_CINS \|\| op == BAM_CDEL) { // your code, you have the length in ol (eg: 101M -> ol == 101) } } } sam_close(f);