Changes

4.5.0

Handle need for allele c to generate is_male data file
ascat.pl accepts abouve file as input for -g

4.4.1

Update base image for performance from htslib 1.11.

4.4.0

Added ascatCounts to produce counts files
Modified ascat wrapper to handle count files as input

4.3.4

Eliminated redundant logic from setup script
Updated Dockerfile to use PCAP-core 5.2.1 as base (Ubuntu 20.04)

4.3.3

Add Rprofile to fix issues with scientific notation

4.3.2

Use lookup tables to translate contig names in case we've stripped out 'chr' in GRCh38
Fix error in *.samplestatistics.txt - GenderChrFound was not being set to Y/N when found but rather the male contig name.

4.3.1

Correct version in dockerfile
Remove development libraries from final build
- Drops image size from 1.33GB to ~1GB

4.3.0

Added a Docker container

4.2.1

Update tabix call to use query_full

4.2.0

Upgrade to core R ASCAT v2.5.1
- applies patch to handle sparse data on a contig (usually Human Y)
Recommend upgrading to alleleCount v4.0.0+
- Switches to fragment based counts instead of read based to prevent double counting.

4.1.2

Updated tabix->query to use tabix->query_full

4.1.1

Fix error in setup.sh testing of alleleCounter version

4.1.0

Modified to use new >= 3.3.0 allelecounter code with dense SNP functionality

2.1.2

Minor fix to usage typo

2.0.0

Now species agnostic provided you can generate a panel of SNPs, approx 1 HET per 2kb is required.
- Tools are included in the package for guided and unguided SNP generation.
- More details can be found in the wiki.
Supports CRAM
Allele count phase is now threaded.

NOTE: Individual scripts called by ascat.pl have been renamed to prevent potential namespace clashes.