v1.2.1

Changed

• Update to ezcharts 0.11.2

v1.2.0

Changed

• Streamlined and simplified the report.
• The per-read stats TSV file is no longer created by default. Instead, several histogram TSV files of read / alignment statistics (read length and mean quality; alignment accuracy and coverage) are output. The original per-read TSV can still be created with the --per_read_stats parameter. It is now gzip-compressed.

Added

• IGV config JSON file to the outputs (in order to visualise the alignments and called variants).

v1.1.2

Changed

• The Summary section of the report now only lists the first 7 sample names and reference files, instead of listing them all.

v1.1.1

Changed

• Reduced the memory requested by some processes to avoid failing in WSL (since there is slightly less memory available in WSL than specified in .wslconfig).

v1.1.0

Changed

• Some formatting changes to github issue template.

Added

• Produce a MMI index file.
• --reference_mmi_file option to use a pre-generated MMI index file as reference.

Removed

• The limit of 20 for the --threads parameter.

v1.0.3

Fixed

• Fix regression in depth plots that concatenated the curves of the different samples, rather than displaying them as a multi-line plot

Changed

• BAM tags from uBAM inputs are now carried over to the resulting BAM files.

v1.0.2

Fixed

• Regression that caused failing on compressed references.
• The alignRead process requesting too little memory in some cases.

Changed

• Reduced the minimum memory requirement from 16 to 12 GB.

v1.0.1

Fixed

• The workflow failing due to commas in reference sequence names.

Changed

• How samples, reference files, and reference sequence names are listed in the summary section at the beginning of the report.

v1.0.0

Added

• Memory requirements for each process.

Changed

• Reworked docs to follow new layout.

v0.6.3

Fixed

• Mangled depth plots when there are multiple reference sequences.
• Report generation failing when there is only a single read or a small number of reads with near-identical mean quality for a sample or reference file.