a3d55b3341
In some cases, the program records were being removed from the BAM headers by the GATK engine before we applied the check for reduced reads (so we did not fail appropriately). Pushed up the check to happen before the PG tags are modified and added a unit test to ensure it stays that way. It turns out that some UG tests still used reduced bams so I switched to use different ones. Based on reviewer feedback, made it more generic so that it's easy to add new unsupported tools. |
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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 | ||