Eric Banks
|
a53e03d525
|
Do not let reduced reads get removed in the contamination down-sampling
|
2012-10-26 02:13:04 -04:00 |
|
Eric Banks
|
72714ee43e
|
Minor patches to get the contamination down-sampling working for indels. Adding @Hidden logging output for easy debugging.
|
2012-10-25 02:47:42 -04:00 |
|
Eric Banks
|
c6b57fffda
|
Added allele biased down-sampling capabilities to the PerReadAlleleLikelihoodMap object, which means that both the UG and HC can use this functionality. Note that it's only available in protected, so GATK-lite users won't be allowed to enable it. Needs more testing.
|
2012-10-24 22:52:25 -04:00 |
|
Eric Banks
|
9da7bbf689
|
Refactoring the PerReadAlleleLikelihoodMap in preparation for adding contntamination downsampling into protected only.
|
2012-10-24 15:49:07 -04:00 |
Ryan Poplin
|
a647f1e076
|
Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.
|
2012-10-20 16:38:18 -04:00 |