samtools c api

[blu78]

Hi all,

Does anyone know if it is possible to use samtools c api to retrieve programmatically all alignments of a readid contained in an indexed bam file?

I am looking for something like the the bam_fetch function but instead of retrieving alignments by chromosome position, I'd like to retrieve alignments by read id.

Thanks in advance for your help.

[Dethecor]

samtools view your_file.bam | awk ' { if( $1 == "your_read_id" ){print $_} } '

assuming that with read_id you meant the sequence name.

You could also implement similar behavior in c / c++ by simply iterating over your file and checking the read_id.

Cheers

[blu78]

Hi, thanks a lot for your answer.

I have to do this necessarily with the c api as this is part of a bigger program and I wanted to understand if it was possible to avoid iterating through the whole file and getting advantage of the index information somehow (i.e. something like the bam_fetch I mean)

Thanks

[maubp]

I don't think the (current) BAM indexes help access reads by their name (just by their mapped position).

[drio]

Depending how the bam is sorted you'll have to traverse the whole file but you can just iterate over all the alignments and save the ones that match the read id you are interested on. Once you have traversed the file you can dump the bam with those alignments.

[jkbonfield]

I too don't think that this is possible in BAM currently without first building your own index.

[blu78]

that's a shame... I will sort alignments by readid and go through the entire file then to retrieve those I am interested in.

Thanks for the help guys