query read by read name

[jay2008]

Hello,
I am using picard library in java.
is it possible to make query for a specific readname in a bam file?

thanks
Yu

[dariober]

Hello,
I am using picard library in java.
is it possible to make query for a specific readname in a bam file?

thanks
Yu

If you just want one or few reads you could do:

samtools view myaln.bam | grep '^myreadname'

Dario

[jay2008]

I meant what the API in picard can be used.

[dariober]

I meant what the API in picard can be used.

Not sure if it is possible in picard. If helpful, consider that you can send the output of picard to stdout using /dev/stdout as output file and then you could pipe it to samtools or grep. If you can be more specific about what you want to achieve you could get more helpful answers...

Dario

[jay2008]

bam file can be sorted in two ways: coordinate and queryname (sorted by read name). bam.query is based on coordinate. I can not find any APIs for bam file sorted by queryname. I guess there should be search APIs...