bam2bakR v3.0.2

Fixes bug in #16 and formatting problems in the example config that could break Snakedeploy.

bam2bakR v3.0.1

Bugfix for spike-in normalization introduced by version 3.0.0 major release

bam2bakR v3.0.0

Major changes are:

• Continuous integration unit testing is now implemented. Includes formatting an linting checks, as well as two separate test runs of bam2bakR, one with bam file input and one with fastq file input.
• Reformatted with snakefmt
• Replaced HTSeq with FeatureCounts, which will provide a massive improvement in pipeline runtime for most use cases.
• Dealt with #8

v2.0.1

Minor bug fixes and documentation updates. Also added a technically missing dependency. Releasing this in preparation for version 3 release, so that users can revert to the older version if necessary.

v2.0.0

Implemented fastq2bakR functionality in bam2bakR. Fastq2bakR takes fastq files as input, trims adapters with Cutadapt, and then aligns reads to a reference using one of three possible aligners:

1. HISAT2 (default)
2. STAR
3. HISAT-3N

bam2bakR 1.0.2

Fixed bug in bam2bakR failing to account for strandedness of the library when quantifying features with HTSeq.

bam2bakR version 1.0.1

This is the second major release of bam2bakR. Changes to previous versions include:

1. Added sorting step prior to fixing read mates to ensure input bam files are properly sorted.
2. Can now run with --use-conda flag rather than installing the pipeline environment manually.
3. Added a strandedness parameter to fix a bug in the mutation counting script.
4. Added a genome indexing step to fix a bug in the SNP calling step.
5. Refactored code to conform to Snakemake best practices.
6. Properly writing standard out/error to log files.
7. Removed unnecessary parameters in config file.
8. Automated calculation of an appropriate fragment size for parallelization of mutation counting.
9. Moved to using bcftools for snp calling rather than deprecated samtools mpileup + bcftools combo
10. Edited .gitignore to facilitate testing and development.

This also includes a bug fix to allow running pipeline within a single conda environment, as well as a bug that prevented deploying this workflow with Snakedeploy.