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query bam with option -H generates malformatted SAM #12

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pontushojer opened this issue Jul 18, 2023 · 1 comment
Closed

query bam with option -H generates malformatted SAM #12

pontushojer opened this issue Jul 18, 2023 · 1 comment

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@pontushojer
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I am using LRez query bam with the option -H to include a header in the output. It however adds a blank line inbetween header and alignments causing the SAM to be malformatted. See example below:

...
@PG	ID:samtools.3	PN:samtools	CL:samtools cat -o final.bam chunks/chrA.calling.bam unmapped.bam	PP:samtools.2	VN:1.12

A00621:130:HN5HWDSXX:4:1368:15555:22889	163	chrA	26885	60	137M	=	26959	137	CAAGTGATCTGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACACGTGTGAACCACCATGCCTGGTCTCTAATTTTTCTGATTCTATAAAATTACATTCTATTTGCTGAAAGAGTACTTTAGAGTTGAAGAAAAAGA	FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF	XF:i:0	PG:Z:MarkDuplicates	RG:Z:1	XG:f:1	NM:i:0	BX:Z:CTTGGTCATTCATACAGTCC-1	MI:i:198
...
@clemaitre
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Hi,

thank you for noticing this. This is corrected.

best,
Claire

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@clemaitre @pontushojer