Dear list,
I would like to programmatically access the samtools library for a C++ program.
Unfortunately, I
cannot figure out how to sort a bam file. Indeed, bam.h states that it offers
ways for sorting but I
did not find a matching function:
------------------------------------------------------------------------
//streams
samfile_t *in = 0, *out = 0;
//open samfile for reading
const char* csampath = sampath.c_str();
in = samopen(csampath, "r", 0);
if (in == 0) {
stop("Fail to open SAM file " + sampath);
}
//open bamfile for writing
const char* cbampath = bampath.c_str();
out = samopen(cbampath, "wb", in->header);
if (out == 0) {
stop("Fail to open BAM file ." + bampath);
}
//read sam and write to bam: adapted from sam_view.c:232-244
bam1_t *b = bam_init1();
while (samread(in, b) >= 0) { // read one alignment from `in'
samwrite(out, b); // write the alignment to `out'
}
bam_destroy1(b);
//close streams
samclose(in);
samclose(out);
//sort bam and build the index
//bam_sort(); //
bam_index_build(bampath.c_str()); //fails if bam is not correctly sorted
------------------------------------------------------------------------
Thanks in advance,
--
Dipl.-Bioinf. Johannes Helmuth, PhD Student
OWL Epigenomics
Max Planck Institute for Molecular Genetics
Ihnestraße 63-73
D-14195 Berlin, Germany
Fon: (+4930) 8413 1173
Web: http://www.molgen.mpg.de/22701/Computational_Epigenomics
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