3724d4e5f3
Note that this tool is still a work in progress and very experimental, so isn't 100% stable. Most of the features are untested (both by people and by unit/integration tests) because Chris Hartl implemented it right before he left, and we're going to need to add tests at some point soon. I added a first integration test in this commit, but it's just a start. The fixes include: 1. Stop having the genotyping code strip out AD values. It doesn't make sense that it should do this so I don't know why it was doing that at all. Updated GenotypeGVCFs so that it doesn't need to manually recover them anymore. This also helps CalculateGenotypePosteriors which was losing the AD values. Updated code in LeftAlignAndTrimVariants to strip out PLs and AD, since it wasn't doing that before. Updated the integration test for that walker to include such data. 2. Chris was calling Math.pow directly on the normalized posteriors which isn't safe. Instead, the normalization routine itself can revert back to log scale in a safe manner so let's use it. Also, renamed the variable to posteriorProbabilities (and not likelihoods). 3. Have CGP update the AC/AF/AN counts after fixing GTs. |
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| .. | ||
| 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 | ||