Mark DePristo 6df96644d9 Unified, standard IndelSummary metrics for VariantEval ... -- Now you always get SNP and indel metrics with VariantEval! -- Includes Number of SNPs, Number of singleton SNPs, Number of Indels, Number of singleton Indels, Percent of indel sites that are multi-allelic, SNP to indel ratio, Singleton SNP to indel ratio, Indel novelty rate, 1 to 2 bp indel ratio, 1 to 3 bp indel ratio, 2 to 3 bp indel ratio, 1 and 2 to 3 bp indel ratio, Frameshift percent, Insertion to deletion ratio, Insertion to deletion ratio for 1 bp events, Number of indels in protein-coding regions labeled as frameshift, Number of indels in protein-coding regions not labeled as frameshift, Het to hom ratio for SNPs, Het to hom ratio for indels, a Histogram of indel lengths, Number of large (>10 bp) deletions, Number of large (>10 bp) insertions, Ratio of large (>10 bp) insertions to deletions -- Updated VE integration tests as appropriate		2012-03-22 21:24:37 -04:00
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net/sf	Fix serious engine bug that could cause reads to be dropped under certain circumstances	2012-02-13 16:25:21 -05:00
org/broadinstitute/sting	Unified, standard IndelSummary metrics for VariantEval	2012-03-22 21:24:37 -04:00