[ADAM-1342] Update CLI docs after #1288 merged. #1343

Merged
merged 1 commit into from Jan 6, 2017

Conversation

Projects
3 participants
@fnothaft
Member

fnothaft commented Jan 6, 2017

Resolves #1342. Adds validation stringency documentation for vcf2adam and adam2vcf. Removes mention of the anno2adam and flatten commands, which were removed in #1288.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Jan 6, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1723/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1723/
Test PASSed.

docs/source/50_cli.md
@@ -330,6 +311,19 @@ options](#default-args). Additionally, `adam2vcf` takes the following options:
* `-single`: Saves the VCF file as headerless shards, and then merges the
sharded files into a single VCF.

This comment has been minimized.

@heuermh

heuermh Jan 6, 2017

Member

Needs a line like

  • -stringency: Sets the validation stringency for various checks. Defaults to STRICT. See validation stringency for more details.
@heuermh

heuermh Jan 6, 2017

Member

Needs a line like

  • -stringency: Sets the validation stringency for various checks. Defaults to STRICT. See validation stringency for more details.

@heuermh heuermh added this to the 0.21.0 milestone Jan 6, 2017

[ADAM-1342] Update CLI docs after #1288 merged.
Resolves #1342. Adds validation stringency documentation for vcf2adam and
adam2vcf. Removes mention of the anno2adam and flatten commands, which were
removed in #1288.
@fnothaft

This comment has been minimized.

Show comment
Hide comment
@fnothaft

fnothaft Jan 6, 2017

Member

Rebased and addressed comment.

Member

fnothaft commented Jan 6, 2017

Rebased and addressed comment.

@AmplabJenkins

This comment has been minimized.

Show comment
Hide comment
@AmplabJenkins

AmplabJenkins Jan 6, 2017

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1724/
Test PASSed.

Test PASSed.
Refer to this link for build results (access rights to CI server needed):
https://amplab.cs.berkeley.edu/jenkins//job/ADAM-prb/1724/
Test PASSed.

@heuermh

heuermh approved these changes Jan 6, 2017

@heuermh heuermh merged commit f3c064c into bigdatagenomics:master Jan 6, 2017

1 check passed

default Merged build finished.
Details
@heuermh

This comment has been minimized.

Show comment
Hide comment
@heuermh

heuermh Jan 6, 2017

Member

Thank you, @fnothaft

Member

heuermh commented Jan 6, 2017

Thank you, @fnothaft

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment