Version 0.4.3

Changes:

• Sample information can now be set by user.
• VCF file can be supplied instead of calling SNPs within Slamdunk.

Version 0.4.2

Bugfixes:

• Fixed version check bug in map module.
• Attribute retrieval fix in core count module.
• Adaptation of splash to raw numbers and more lenient on RA:Z tags
• Bugfix in read length checking step from sys.maxint to sys.maxsize

Version 0.4.1

Bugfixes:

• float to int fix in multithreaded snp step

Version 0.4.0

Major refactoring:

• Rewriting source for full python3 compatibility
• All dependencies now provided externally, *environment.yml file added to pull in dependencies from Bioconda
  • NextGenMap v0.5.2 -> v0.5.5. Takes care of flipped basequalities in supplementary alignments.
  • Varscan2 v2.4.1 -> v2.4.4
  • Samtools v1.9 -> v1.10
  • RNASeqReadSimulator by Wei Li added as subtree
• Dockerfile moved and updated to run with miniconda
• Travis-CI testset updated.

Version 0.3.4

Bugfixes:

• Reverse strand A->G SNP coordinates offset fixed.

• Mismatch of string to int in key search fixed for summary.

Version 0.3.3

Bugfixes:

• Mutation type bugfix in MPTagToConversion fixed
• Deduplicated bam file properly closed for indexing
• alleyoop snpeval also works now without snp sets
• Chromosome retreival fix for pysam
• dplyr dependencies removed (Bioconda)

Version 0.3.2

Changes:

• Bioconda: Slamdunk recipe added. Slamdunk now available via conda from v0.3.2!
• Symlink ngm -> nextgenmap/bin/ngm-0.5.2/ngm replaced by hard copy for bioconda-utils build compatibility.

Version 0.3.1

Changes:

• Upgrade Samtools 1.3.1 -> Samtools 1.9 for upcoming bioconda build.

Bugfixes:

• pysam-0.15.0.1 region retreival fix. (dashed chromosomes allowed now)
• NGM permission fix to allow Singularity image build directly from Docker hub.

Version 0.3.0

Changes:

• Travis-CI testing added.
• Automated versionable Docker container builds.
• Static 2 T>C conversion cutoff multiTCSTringency parameter replaced by dynamic conversion-threshold parameter
• Positional track module added to Alleyoop to produce genome-wide positional T>C conversion rate bigWigtracks
• Read-separator module added to Alleyoop to separated T>C reads from non T>C reads into bam-files.
• Docker base image set to ubuntu:18.04

Bugfixes:

• Supplementary alignment flags unset in filtered bam
• Fixed numpy version removed to satisfy pandas dependency
• Minimum baseQ filter now inclusive which is the expected behaviour
• Reference check for short chromosomes introduced
• Backwards compatibility to pysam 0.8.3 introduced

Version 0.2.4

Changes:

• License updated to AGPLv3
• Deduplicator now only marks duplicates instead of removing them. Useful for deduplication QA like dupRadar. Allows for deduplication of T>C-fraction of reads only.
• Singularity build-file branch added.

Bugfixes:

• readInRegion fixed: Switched from fetch(region="chr:start-end" (1-based) to fetch(reference=chr, start=start, end=end) (0-based). Intervals close to the ends of a chromosome are now correctly handeled and not skipped.
• Hotfix to fix executable permissions on some R plotting scripts
• Fixed alleyoop collapse to ignore all MLE columns for now
• R package dependencies fixed for IMP cluster
• include_package_data removed for proper contrib import