Version 0.2.5

Support upstream filtering/downsampling in previous workflow tasks:

• Can supply an additional BAM file as input to slow metrics
• Extra metadata fields to record upstream filtering

Version 0.2.4

Additional metadata fields for merged BAM files

Version 0.2.3

• GP-2234 Export picard2 duplication metrics histograms
• GR-968 Aggregate and export picard duplication metrics calculated from merged libraries.
• GR-986 Run a fast subset of metrics for RNASeqQC

Version 0.2.2

Add support for picard MarkDuplicates metrics input that is missing ROI histogram.

Added:

• GR-908 Support missing ROI histogram

Version 0.2.1

Add support for picard 2.21.2 MarkDuplicates metrics histogram input.

Added:

• GR-883 Support picard 2.21.2 input

Version 0.2.0

• Increment minor version as we deploy bam-qc-metrics for production testing
• GP-2126 bugfix for location of VERSION file

Version 0.1.8

• Bugfixes GP-2115
• Correctly update "undetermined reads" dictionaries
• Run samtools in subprocess instead of pysam.stats; enables error handling

Version 0.1.7

• Complete set of metrics for first production release
• Additional bedtools coverage metrics
• Downsample to absolute target number of reads (instead of relative proportion)
• Added logging and profiling, and improved tmpdir handling

Version 0.1.6

Bugfix; copy the VERSION file to the installation directory in setup.py

Version 0.1.5

• GP-2040 Extensive refactoring; clear separation of fast/slow metrics
• GP-2038 Report software versions in output
• GP-2037 Count mismatches by cycle using samtools stats instead of the CIGAR string
• Placeholders for additional bedtools metrics
• Various minor bugfixes; see CHANGELOG.md