USeq Source Code

Added option to NBP to parse bam files, updated the bisulfite tutorial/ user guide to recommend dropping dups with MarkDuplicates.jar

Mods to the MethylationArray apps, corrected a minor bug, added non paired functionality, updated the docs.

Fixed an issue that was causing a null pointer error due to lack of a genome build string.

Final modifications to the VCFComparator. This is ready to go.

Lots of mods to support more efficient loading of vcf files for the VCFComparator. New app for scanning defined regions of methylation array data.

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