Version 0.2.3

Bugfixes:

• Hotfix to include README.md in sdist packaging
• Hotfix to fix executable permissions on some R plotting scripts
• Fixed alleyoop collapse to ignore all MLE columns for now

Version 0.2.2

Changes:

• Slamdunk supports now MultiQC <http://multiqc.info/>_ report creation
• Default set to local mapping
• Base-quality cutoff implemented throughout the entire slamdunk / alleyoop workflow
• BAQ computation disabled for samtools mpileup
• Dedup now supports selection of reads containing a defined # T>C conversions
• All documentation moved to gh-pages branch for slicker repo
• CPMs now normalized to filtered reads
• Docker image now build automatically to head revision
• Official webpage introduced instead of readthedocs.org hosting
• Evaluation module for count files added to splash

Bugfixes:

• PCAs for single sample working now
• Dedup working again
• Sample files may contain empty lines now

Version 0.2.1

Changes:

• PCA will be added to alleyoop summary if count folder is provided
• Reads in UTRs will be added to alleyoop summary if count folder is provided
• Comment tags added to summary, rates, utrrates, tcperreadpos, tcperutrpos to be recognized by MultiQC http://multiqc.info/
• NextGenMap udated to version 0.5.2
• Slamdunk now checks NextGenMap version
• Simulation module (splash) added: simulates slamdunk samples from a set of UTRs (BED file) and evalutes results computed by SlamDunk. See splash –help for more information
• -i/–sample-index is now 1-based instead of 0-based
• Columns for conversion rate confidence interval added to count files (not used yet)
• Filter summary integrated into log
• Added sample names now in globalRatePlotter

Bugfixes:

• Number of sequenced reads fixed for BAM files computed with -ss/–skip-sam option
• NextGenMap memory leak fixed

Version 0.2.0

Due to major changes v0.2.0 is not compatible with v0.1.0. Please rerun alle your samples with slamdunk 0.2.0!

Changes:

• Option to supply sample info via samplesheet instead of plain raw reads added.
• Added @rg tag to bam files containing sample info for best-practice and easier summary calculation.
• Flagstat files removed.
• –skip-sam flag added to only output bam.
• –sample-index flag implemented for cluster distribution.
• Multi-TC stringency now also available for utr rate plots.
• stats prefixes removed from alleyoop modules.
• Alleyoop summary module implemented. Summary contains sample infos (if specified via samplesheet) and number of sequenced, mapped and filtered reads.
• Alleyoop merge module allows now merging upon column names.
• Sample info and reference + checksum now documented in tcount files.
• Version.py added.

Bugfixes:

• NGM interspersed order of multimappers fixed.
• Random seed from filter module deleted.
• Alleyoop rates display error of bars higher than ylim fixed.
• Min base quality now again propagated to all modules. Auto-scaling error fixed in globalRatePlotter.

Version 0.1.0

First slamdunk pre-release to test behaviour on the cluster and PyPI.