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The current gbam writer expects a BAMRawRecord. Because of that I converted the SamRecord to BAMRawRecord rather than directly passing the sam record. I felt it would be risky to change the stable writer code to support SAM directly. But if there are "considerable" performance issuse, we may consider avoid creating BAMRawRecords. WDYT @AndreaGuarracino |
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Yeah, if we become too slow, we can consider that!
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Subject: Re: [NickRoz1/gbam] SAM input to gBAM (PR #27)
[https://avatars.githubusercontent.com/u/41409951?s=20&v=4]chris7716 left a comment (NickRoz1/gbam#27)<#27 (comment)>
Can we avoid going through BAM records? Sent from Outlook for Androidhttps://aka.ms/AAb9ysg
The current gbam writer expects a BAMRawRecord<https://github.com/NickRoz1/gbam/blob/master/gbam_tools/src/writer.rs#L125>. Because of that I converted the SamRecord to BAMRawRecord rather than directly passing the sam record. I felt it would be risky to change the stable writer code to support SAM directly. But if there are "considerable" performance issuse, we may consider avoid creating BAMRawRecords. WDYT @AndreaGuarracino<https://github.com/AndreaGuarracino>
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Logic
SAM > GBAM > SAM records are identical. But there is an issue in the rust GBAM reader code how we set SAM header. We do not set AS: tags in the header when reconverting gbam to bam. Because of that reconverted bam's header is not identical to the orginal bam's header. https://github.com/NickRoz1/gbam/blob/master/gbam_tools/src/bam/gbam_to_bam.rs#L21-L24