5afcc8e05f
Following reviewers comments the command line interface has been simplified.
All extra strict validations are performed by default (as before) and the
user has to indicate which one he/she does not want to use with --validationTypeToExclude.
Before he/she was able to indicate the only ones to apply with --validationType but that has been scrapped out.
Stories:
- https://www.pivotaltracker.com/story/show/68725164
Changes:
- Removed validateType argument.
- Improved documentation.
- Added some warnning log message on suspicious argument combinations.
Tests:
- ValidateVariantsIntegrationTest#*
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| .. | ||
| VectorPairHMM | ||
| c | ||
| chainFiles | ||
| doc | ||
| external-example | ||
| gatk-framework | ||
| gatk-package | ||
| gatk-queue-extgen | ||
| gsalib | ||
| java/config | ||
| package-tests | ||
| perl | ||
| queue-framework | ||
| queue-package | ||
| repo | ||
| sting-root | ||
| sting-utils | ||
| pom.xml | ||