USeq Source Code

1. fixed code to skip folders missing .email.txt file
2. Added logging

1. Fixed bug in naming convention of file to find

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)
9. Added code to catch "None" for Read1Adapter and Read2Adapter
10. Changed permissions of newly-created tomato/job/ folders to 777
11. Fixed broken path to fastqc app run prior to alignment
12. Fixed a soft-linking error to be more explicit with file matching
13. Made the code more readable by using StringBuilder to construct the cmd.txt file
14. Fixed a few potential errors with constructing the cmd.txt file
15. Added logging

DefinedRegionDifferentialSeq
* Added internal check to remove edgeR analysis and proceed if the app throws errors.
SamSubsampler
* New app to subsample a sam/bam file after filtering and randomizing. Needed for comparing read coverage graphs.
BisStat
* Added option to export base level log 2 ratio of fraction methylation in T vs C graphs.
* Renamed graph folders to indicate Base or Window level data

MethylationArrayDefinedRegionScanner
* Modified app so it works with non even numbers of t and c
SamParser
* Modified the way the mid point of an alignment is calculate. It is now the alignment start + 1/2 the read length. Did this to avoid problems with splice junction reads.
* Set the bam file reader stringency to silent.

Added additional reporting options to VCF reporter. Fixed typos in ParseExonMetrics

edu.utah.tomato: lots of fixes and improvements
edu.utah.seq.vcf: Added automatic vcf chunking to improve memory usage
edu.utah.diagnostics: Metrics are now reported as html and can be merged. Fixed figures.
edu.utah.seq.data: Fixed error in CalculatePerCycleErrorRate. Only encountered when the number of phiX sequences is huge.

Added back in apps that we're compiling to the build props.

RNAEditingScanSeqs
* Added a minimum base fraction edited option to app to restrict what base observations are allowed into the analysis.
RNAEditingPileUpParser
* Fixed a bug where the parser was counting all of the reference reads (both plus and minus) when scoring a base for editing instead of just reads mapping to the matched strand when a stranded parsing was selected.

Added an option to reset the maximum alignment score, needed for parsing Evan Johnson's gnumap alignments.