gowtham | 8 Mar 20:41 2013

Writing alignment objects read via Bio::DB::Sam

Hi Every One,
I'm using Bio::DB::Sam->new(-bam='') method to read a bam file. And I am
able to query individual values of each alignment record. For example
'XM','AS', and 'AS' tags, or alignment start end positions etc. After
filtering these records for some values (eg, mismatches), i would like to
write them back into a "SAM" (preferable BAM) format.

I am not able to find a method that writes the record. Can someone help me
with this?

Though, I am able to open a new bam file for  writing using
Bio::DB::Bam->open(my.bam, 'w'), I dont know how to convert the SAM
alignment i read from (Bio::DB::SAM) to be written using this.

write1() does not accept alignment object read by Bio::DB::SAM, it accepts
objects read only by Bio::DB::BAM.

Thanks very much in advance,


Bioinformatics Systems Programmer.
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Phone : LAB 206-256-7188 (direct).