From aeac8f7b97f606a357c869cbe12cb2da133ddec0 Mon Sep 17 00:00:00 2001 From: Demetri Nicolaou Date: Thu, 6 Aug 2020 09:13:48 -0700 Subject: [PATCH] cmd/bio-bam-sort: fix bio-bam-sort -sam documentation Summary: Fix documentation for `bio-bam-sort -sam ...` to state that `-sam=true` by default and if a user wants to sort BAM records, they must explicitly state `-sam=false`. For more context on this change, see D47837. Test Plan: Proofread documentation changes. There are no code changes to test. Reviewers: cchang Reviewed By: cchang Subscribers: sbanville, ayip Tags: #methylation_pipeline Maniphest Tasks: T39542 Differential Revision: https://phabricator.grailbio.com/D47856 fbshipit-source-id: 67c1f09 --- cmd/bio-bam-sort/cmd/main.go | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/cmd/bio-bam-sort/cmd/main.go b/cmd/bio-bam-sort/cmd/main.go index 479dad7..6a71b2b 100644 --- a/cmd/bio-bam-sort/cmd/main.go +++ b/cmd/bio-bam-sort/cmd/main.go @@ -100,9 +100,9 @@ sorting and merging. The command reads a sequence of bam or sam records from input, sorts them, and produces file (note: this is NOT a BAM formatted file, - it is a shard file). If is '-', records are read from stdin. With - -sam flag, the records are assumed to be in SAM format. Else, it is assumed - to be in BAM format. + it is a shard file). If is '-', records are read from stdin. If + -sam=false, records are assumed to be in the BAM format. Else, records are + assumed to be in SAM format. 2. bio-bam-sort -bam