How to get a list of aligned read and reference positions using samtools
I am trying to convert a python script that manipulates bam files, to C++. However, I couldn't find out how can I get a list of aligned query and reference positions using samtools. I want to get reads from a region and for that, I used this link: htslib C API: getting reads from region
But I cannot find a way in samtools to get the list of aligned query and reference positions. In pysam "get_aligned_pairs" returns this list. How can I extend the code in the link I mentioned to do this in samtools?
Thanks
• 1,731 views
•
link
updated
by
Ram
•
written
by
Aref.Ariyapour •
•
written
by
Aref.Ariyapour •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Extracting reads from bam file using samtools view for non-standard reference names
written by JmzW •
-
How can I find reads that have multi-mapped with multiple genes overlapping in the same region
written by Berk •
-
Extract aligned reads from a bam file for only selected coordinates
written by star715 •
-
Extract reads that are contained entirely within a give region
written by george.wiggins •
-
Changing n_lvls in htslib hts.c, or, samtools index error "Numerical result out of range"
written by A Soggy Waffle •
-
Is there any C API documentation for HTSLIB?
written by chen
-
Mate pair positions using pysam
written by QVINTVS_FABIVS_MAXIMVS
-
htslib C API: getting reads from region
written by QVINTVS_FABIVS_MAXIMVS
-
convert list of positions to BED file
written by lovestowell •
-
How Many Reads In A Bam File Are Aligned To An Arbitrary Region
written by David Quigley
samtools view in.bam “chr1:100-1000”
Can you please elaborate a bit more? I want to do it in c. In each read inside while loop ("sam_itr_next(in, iter, b)") I want to get the list of pairs.