• 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)