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sam/header/record: Header record with group order is serialized incorrectly #122

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zaeleus opened this issue Oct 25, 2022 · 0 comments
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zaeleus commented Oct 25, 2022

However I did find a file that noodles was unable to re-read back. This was its own generated file. Samtools can decode it fine, so it's maybe a noodles decode issue rather than encode one. That seemed related to the presence of GO:query in the input SAM header.

@HD	VN:1.6	SO:unsorted	GO:query
VP2-06:112:H7LNDMCVY:1:1273:1687:24048	77	*	0	0	*	*	0	0	TTGCCCAGGCTGGTCTTGAATTCACGGGCTCAAGCCATCCTCCTAGCTGAGCCTCCTGAGTAGCTGGGATTACAGGTGTGAGCCATTGCACCCAACTGGTATAGCCACGTTAGAAAACAGTCTGGCAGTTTCTCAAAAGGCTAAATGTACA	EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE3EEEEEEEEEEE3EEEEEE3EEEEEEEEEEEEEEEEEEEEEEEEEEEEEE3EEEEEEEEEEEEEEEE3EEEEEEEEEEEEEEEEEE3E3EEE3-E3-E3EE

I can add this as a separate issue if you prefer as I doubt it's CRAM 3.1 related. Removing the GO:query fixes this round trip.

Originally posted by @jkbonfield in #107 (comment)

@zaeleus zaeleus self-assigned this Oct 25, 2022
@zaeleus zaeleus added bug Something isn't working sam labels Oct 25, 2022
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