Subject: Writing alignment objects read via Bio::DB::Sam
Date: Friday 8th March 2013 19:41:38 UTC (over 4 years ago)
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, Gowthaman -- Gowthaman Bioinformatics Systems Programmer. SBRI, 307 West lake Ave N Suite 500 Seattle, WA. 98109-5219 Phone : LAB 206-256-7188 (direct).