2.26.2

• Changed calculation of call rate to account for zeroed out SNPs. (#1711)

2.26.1

• Updated documentation for MarkDuplicates.java (#1704)
• Fixed a tiny typo in CollectWgsMetrics (#1705)
• Added adapter and quality trimming to IlluminaBasecallsToFastq. (#1646)
  ** Note that this changes the default behavior of IlluminaBasecallsToFastq to trim adapters.
• Adjusted handling of missing data situations in CheckFingerprints (#1700)

2.26.0

• Make cram valid input to remaining CLPs (#1622)
• Add on the fly demux and speed up barcode matching. (#1649)
• Cleaned up some variable names and order in the alignment metrics code. (#1707)
• Added some more skew-resistent metrics for read length (#1706)
• Fix typo in usage (#1703)
• HaplotypeMap bug fix (#1702)
• Fix bug in CollectSamErrorMetrics (#1618)

2.25.7

• [bugfix] fix underflow in HaplotypeProbabilitiesFromContaminatorSequence (#1697)
• [bugfix] and nio access in Fingerprinting code (no need to panic) (#1694)

2.25.6

• [bugfix] Fix small data race condition (#1690)
• [bugfix] Pass MAX_RECORDS_IN_RAM to BasecallsConverter (#1687)
• Only read the cbcl header once the tile is about to be cached and then close the streams. (#1686)
• Added ref to software catalogs to citation section (#1606)
• Addressing Integer comparison bug yeilding deflated rrna counts (#1680)

2.25.5

• Created CreateExtendedIlluminaManifest tool (#1667)
• SortGff tool (#1531)
• Handle error case in interruptAndShutdownExecutors. (#1678)

2.25.4

• Allow for no barcode files case. (#1675)
• R Chart/PDF output filenames escape '%' with '%%' (#1671)

2.25.3

• Add validation of existence of input directories (#1673)
• [bugfix] Fix an issue with cbcl parsing when barcodes files are in a different directory from basecalls. (#1672)
• Only run PR build, not the branch build (#1656)
• Fix: getCumulative R method optimized (#1659)

2.25.2

• Throw an exception if one of the pooled threads has an error. (#1663)
• Delay data provider instantiation to avoid caching too many tiles when using cbcls. (#1658)
• Added multi-lane support to BasecallsConverter (#1642)

2.25.1

• Use AsyncWriterPool for Fastq writing. (#1645)
• Merge branch 'master' into rz_rnaseqmetrics_parameterize_endbias_length
• Update to htsjdk 2.24.1 (#1655)
• Merge branch 'rz_rnaseqmetrics_parameterize_endbias_length' of https://github.com/watchmaker-genomics/picard into rz_rnaseqmetrics_parameterize_endbias_length
• 1. Added an additional constructor for RnaSeqMetricsCollector to be backwards compatible. 2. Added a static default endBias in the RnaSeqMetricsCollector to define the default value, and reference that in the constructor and in CollectRnaSeqMetrics
• Merge branch 'master' into rz_rnaseqmetrics_parameterize_endbias_length
• 1. Spellcheck.
• Add ConvertHaplotypeDatabaseToVcf clp (#1648)
• 1. Addressed test description comment. 2. Parameterized test start and stop positions. 3. Cleaned up whitespace.
• 1. Updated test cases to derive from DataProvider 2. Updated documentation to mention the role of end bias bases in bias calculation and coverage metrics filtering transcripts under the end bias length.
• Change docker base image for security reasons. (#1654)
• Add sample -> individual map capability to CrosscheckFingerprints (#1643)
• Updated the unit test to explicitly call the parameters for each case.
• Added an option to specify an end bias into a transcript replacing the constant PRIME_BASES (100 nt) variable. The default of this parameter set to the previous fixed value.
• Fix multi-tile bcl file faking (#1640)
• A tool to convert BafRegress output to a Picard metrics file. (#1597)
• Parse version directly from tile metrics instead of using a clp flag. (#1633)
• Add AppSec GitHub Trivy Action (#1634)
• Update RefFlatReader.java (#1530)