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fredjarlier avatar fredjarlier commented on June 9, 2024

Action 1: Adapt mpiSort.c management of the SAM header to fit the output of mpiBWAByChr new design (version 1.3). Especially with mpiSORT -u

Action 2: Modify the parser.c to write fragment both in chrN.sam and in discordant.gz

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fredjarlier avatar fredjarlier commented on June 9, 2024

commit 1: 592fd70

Action1 and Action2

todo: Update documentation

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fredjarlier avatar fredjarlier commented on June 9, 2024

review on action 2: discordant.gz not necessary in uniq mode. We can keep the discordant in the chrN.bam (samtools markdup is ok with that). After mpiBWAByChr + samtools fixmate no unmapped nor discordant are found.

action 3: now the chrID must be passed after -u option to mpiSort

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fredjarlier avatar fredjarlier commented on June 9, 2024

action 2 and 3 done in commit a3436bf.

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fredjarlier avatar fredjarlier commented on June 9, 2024

Action 4: Update the doc

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