b4f482a421
-- Made CountReadsInActiveRegions Nano schedulable, confirming identical results for linear and nano results -- Made Haplotype NanoScheduled, requiring misc. changes in the map/reduce type so that the map() function returns a List<VariantContext> and reduce actually prints out the results to disk -- Tests for NanoScheduling -- CountReadsInActiveRegionsIntegrationTest now does NCT 1, 2, 4 with CountReadsInActiveRegions -- HaplotypeCallerParallelIntegrationTest does NCT 1,2,4 calling on 100kb of PCR free data -- Some misc. code cleanup of HaplotypeCaller -- Analysis scripts to assess performance of nano scheduled HC -- In order to make the haplotype caller thread safe we needed to use an AtomicInteger for the class-specific static ID counter in SeqVertex and MultiDebrujinVertex, avoiding a race condition where multiple new Vertex() could end up with the same id. |
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| .. | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| compression/reducereads | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| haplotypecaller | ||
| indels | ||
| phasing | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||