CRAM: embedded references + multi-slice implies error

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#503 opened on Apr 7, 2017 0 comments 0 reactions 1 assignee View on GitHub

@jkbonfield is already working on this.

Since Apr 7, 2017.

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Description

$ samtools view -O cram,seqs_per_slice=100,slices_per_container=3,embed_ref mpileup.1.bam -o _.cram
$ samtools view -f 0xffff _.cram
ERROR: md5sum reference mismatch for ref 0 pos 581..1515
CRAM: 4e96f155b96b5a96edd94baa663201f1
Ref : 83916a0a333f001225279539abe685fe
Failure to decode slice
[main_samview] truncated file.

With slices_per_container=1 it's fine, as is without embed_ref or with no_ref option. (Scramble has the same bug too.)

Dominant language: C
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