brentp / cigar Goto Github PK
View Code? Open in Web Editor NEWsimple library for dealing with SAM cigar strings
License: MIT License
simple library for dealing with SAM cigar strings
License: MIT License
Hi,
I just found your efficient library to process CIGAR Strings into Python Lists.
Do you know a Python-way to calculate the rlen attribute, which is internally computed by samtools in Code ?
hts_pos_t bam_cigar2rlen(int n_cigar, const uint32_t *cigar)
{
int k;
hts_pos_t l;
for (k = l = 0; k < n_cigar; ++k)
if (bam_cigar_type(bam_cigar_op(cigar[k]))&2)
l += bam_cigar_oplen(cigar[k]);
return l;
}
My first try is :
c=Cigar('20M5I10M3I5M')
sum([x[0] for x in c.items() if x[1] == "M" ])
Here's an example:
print("3M1D137M",cigar.Cigar("3M1D137M").mask_left(4).cigar)
Which will yield:
3M1D137M 5S136M
Which is incorrect, as the original "3M1D137M" string has query sequence length 140, but the left-masked query sequence length of "5S136M" is 141.
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