USeq Source Code

Autoaligner:
1. added code to move fastQC output to QC directory

Autoaligner:
1. Changed soft-linking of input fastq files to separate method, with explicit file matching
2. Added code to create new rawAlignment, processedAlignment, coverageTracks, and logs dirs when new analysis report dir is created.
3. Added code to remove split fastq bisulfite files after alignments have completed
4. Added a new field (column) for fastq file name in the Sample class to parse from the fresh data report
5. Fixed bug where output format wasn't specified as .sam for genomic sequences
6. Changed code to explicitly call filenames
7. Added code to Sample class to parse additional field for sequencing adapter from fresh data report
8. Added fields for SequenceLane, Read1Adapter, Read2Adapter, File(path)
Sample:
1. Added 4 new fields (w/ getters/setters) from autoalign report
2. Removed redundant, unused fields
Ketchup:
1. Fixed it so soft links are not followed or considered for file deletion

Modified app to gzip temp files and when a header is provided to directly write out the results without an intermediate file. Should cut down on disk usage.

Alex William's (Gladstone) customization of the DRDS. Lots of mods.

Mods for the Methylation Array Scan Seqs and VCF classes

Checkin of an app for window scanning methylation array data for DMRs.

Lots of mods to support the VCFComparator app.

Lots of mods to support the VCFComparator app.

Added option -b to both SamTranscriptomeParser and RNASeq. This option flips the strand of both reads. Note that this is independent of the flip second strand option, selecting both will leave the second strand read unchanged.

Added option for stranded analysis into DefinedRegionRNAEditing