2.18.12

• 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)

2.18.11

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

2.18.10

• 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.

2.18.9

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

2.18.8

• upgrading htsjdk 2.15.1 -> 2.16.0 (#1184)

2.18.7

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

2.18.6

• 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)

2.18.5

• 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)

2.18.4

• DSDEGP-2199 Add new MakeVcfSampleNameMap tool. (#1160)
• Move setting of TMP_DIR prior to inflater/deflater check. This ensures that java.io.tmpdir is set (which is used when checking if we have space for using the intel deflater/inflater). Currently it will always check system temp dir. (#1165)
• Jc fix executor exception handling (#1163)

2.18.3

• Add arguments and reporting around recovering REF/ALT swapped alleles (#1151)
• Added reverse cycle and base dir lookup for tile metrics. (#1158)
• Allow processing of a single tile. Append tile integer to output filename to avoid overwrites by multiple tiles. (#1154)
• Add to gradle build pre-requisites check (#1156)
• Integrate @ExperimentalFeature and @BetaFeature tags (#1094)
• Yf fix infinite loop md (#1147)
• Make picardcloud accessible in docker image (#1153)
• Remove sbt & Eclipse files from gradle project (#1137)