2.26.11

• In GtcToVcf, set infinite values to missing ('.') in the VCF. (#1777)
• Correct logic to have ExtractBarcodesProgram properly match for all Ns (#1775)
• Cluster Visualization Python Script (#1701)
• Detect worker thread exception sooner, and stop other workers. (#1772)

2.26.10

• Update log4j to v2.17.1 (#1768)

2.26.9

• Update log4j to v2.17 (#1766)

2.26.8

• Update Picard to Log4J 2.16.0 (#1762)

2.26.7

• Upgrade Barclay. (#1760)
• Update log4j version 2.15 to address CVE-2021-44228
• Clarified comment for purpose of GatherVcfs (#1758)

2.26.6

• Fix error in Picard jar packaging that prevented it from running under Java 11. Make the shadowJar multi-release. (#1749)
• Fix picard doc on java 11 (#1750)
• Change IlluminaBasecallToFastq to make the parameter ADAPTERS_TO_CHECK to be null by default (#1745)
  ** Note that this reverts the behavior of IlluminaBasecallsToFastq back to what it was in Picard release 2.26.0 and before.
• Fix data provider for IlluminaBasecallsToSamTest (#1752)

2.26.5

• Fixed bug in initialization of ExtractIlluminaBarcodes perfect score array. (#1744)
• Removed deprecated parameter 'IS_NOVASEQ' from CollectIlluminaLaneMetrics. (#1736)
• Updated the GKL version to 0.8.8 (#1733)
• Added validation for existence of .bpm file to CompareGtcFiles (#1743)

2.26.4

• Fixed a bug in IlluminaBasecallsToFastq where ADAPTERS_TO_CHECK could not be set as a CLP argument. (#1740)
• Fixed a bug in GtcToVcf where where SOURCE fields populated from the Illumina manifest that contain a semicolon may be incorrectly populated in the INFO field of the VCF (#1738)
• Updated CombineGenotypingArrayVcfs to handle differences in INFO:SOURCE field of a VCF generated by GtcToVcf (#1739)
• Added more logging to IlluminaBaseCallsToSam/Fastq (#1735)

2.26.3

• Added CLP that can combine multiple QualityYieldMetrics files (#1717)
• Added description of the gtcCallRate field in the VCF Header. (#1730)
• If deprecated parameter MAX_READS_IN_RAM_PER_TILE is specified, have IlluminaBasecallsToFastq set MAX_RECORDS_IN_RAM appropriately. (#1726)
• Minor updates: https, new urls, license year (#1723)

2.26.2

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