@snovod snovod released this Sep 12, 2018 · 5 commits to master since this release

Assets 4
  • DSDEGP-2749: too many tokens exception in download genotypes (#1226)

@snovod snovod released this Sep 10, 2018 · 6 commits to master since this release

Assets 4
  • upgrade to htsjdk 2.16.1 (#1224)
  • now starting from the origin commit
  • Fix output file naming
  • Fix to ValidateSamFile to warn when NM validation occurs without reference (#258) (#1220)
  • improves MarkDuplcates documentation, fixes #1087 (#1088)
  • Installation of r-base in Docker Image allows RExecutor to work (#1198)
  • Warning message about upcoming command line syntax transition. (#1204)
  • CreateSequenceDictionary support for alternative names (@SQ-AN) (#1127)
  • Fix GenotypeConcordance bug writing spanning deletion (#1210)
  • The method createTemporaryIndexedVcfFromInput(File, String) was changed (#1213)

@snovod snovod released this Aug 28, 2018 · 17 commits to master since this release

Assets 4
  • Diagnose missing barcodes in ExtractIlluminaBarcodes instead of throwing NPE. (#1212)
  • FixVcfHeader can now add missing FILTER header lines. (#1205)
  • Yf fix scatter with overflow mode (#1206)
  • Added options to IlluminaBasecallsToSam (#1162)

@snovod snovod released this Jul 23, 2018 · 21 commits to master since this release

Assets 4
  • Fix an issue where the google NIO code would try to load even when the NIO library wasn't present. (#1201)

@snovod snovod released this Jul 19, 2018 · 22 commits to master since this release

Assets 4
  • Tidy up TileMetricsOutReader a bit. (#1200)
  • MarkDuplicates to accept Query-Grouped (not Sorted) input and a slight change in tiebreak order
  • Adding a LIBRARY field to the umi metrics file in UmiAwareMarkDuplicatesWithMateCigar (#1193)
  • Adding error in LiftoverVcf if reference dictionary does not exist (Issue #1157) (#1189)
  • new CLP: CollectSamErrorMetric (#1180)
  • Merge branch 'epam-ls_bug_collectmultiplemetrics_no_refflat' of https://github.com/EpamLifeSciencesTeam/picard into epam-ls_bug_collectmultiplemetrics_no_refflat
  • Bug when no refflat file input in CollectMultipleMetrics fixed. New test for CollectMultipleMetrics.

@snovod snovod released this Jul 2, 2018 · 33 commits to master since this release

Assets 4
  • DSDEGP-2516 Make RevertSam resilient to read groups with no reads. (#1191)

@snovod snovod released this Jul 2, 2018 · 34 commits to master since this release

Assets 4
  • upgrading htsjdk 2.15.1 -> 2.16.0 (#1184)

@snovod snovod released this Jun 7, 2018 · 35 commits to master since this release

Assets 4
  • pass all tile metrics files to parser and id correct one there

@snovod snovod released this Jun 4, 2018 · 53 commits to master since this release

Assets 4
  • Bump to Intel GKL version 0.8.5. (#1182)
  • upgrade htsjdk to 2.15.1 (#1181)
  • Fixes intermittent failures in TheoreticalHetSensitivityTests. (#1178)
  • remove non-ascii character
  • Added forgotten (test) class that tests MarkDuplicates on queryname sorted input. (#1174)

@snovod snovod released this May 24, 2018 · 59 commits to master since this release

Assets 4
  • Generalization of Theoretical Het Sensitivity to handle arbitrary all… (#1144)
  • Allowing static fields in MergableMetrics to be not annotated (#1173)
  • Update htsjdk (#1171)
  • Use the awaitThreadPool from new util class (#1169)
  • Avoid overflow when computing barcode metrics. (#1167)