Skip to content

Commit

Permalink
cmd/bio-bam-sort: fix bio-bam-sort -sam documentation
Browse files Browse the repository at this point in the history
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
  • Loading branch information
demetrin authored and Alexander Yip committed Aug 17, 2020
1 parent eb33ecf commit aeac8f7
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions cmd/bio-bam-sort/cmd/main.go
Original file line number Diff line number Diff line change
Expand Up @@ -100,9 +100,9 @@ sorting and merging.
The command reads a sequence of bam or sam records from input, sorts them,
and produces file <output.sortshard> (note: this is NOT a BAM formatted file,
it is a shard file). If <input> 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 <input> 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 <foo.bam> <input.sortshard...>
Expand Down

0 comments on commit aeac8f7

Please sign in to comment.