Slamdunk

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

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.

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