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Published 20 hours ago • verified publisher icon samtools

Fixes involving CRAM and header API for long references.

Open jkbonfield opened this issue 4 years ago • 1 comments

This is obviously only partial because we need CRAM4 for long reads, but it's now better at reporting errors and also now copes correctly with the cases inbetween 28-bit and 32-bit sizes for long cigar ops.

The header API has also had some fixes, which were discovered in the process of updating CRAM. The main culprit was sam_hdr_dup which didn't honour h->sdict.

jkbonfield avatar Nov 15 '19 12:11 jkbonfield

Moving the code to sam_hdr_update_target_arrays looks to have fixed the problem in a more elegant way. Thanks.

jkbonfield avatar Nov 18 '19 16:11 jkbonfield