USeq Source Code

Lots of mods and new apps. More tweaks to the json output from Sam2USeq. More options for outputing data from mpileup files. Fixes to VCF classes to work with DNANexus vcf calls on NIST datasets. Finally fixed the java 1.8 compatibility issue with GenomicRegions. Lastly, new app for inserting barcodes from a third fastq file into paired fastq datasets.

Added ability to parse multi sample mpileup files

Hmm, can't seem to upload a release to SF's Files?! Was failing Friday. Moving the site to GitHub......

Sam2USeq
* Added a failed bed region output for those target bases with less than the indicated depth. Good for identifying holes in particular locations, and deletions.
Sam2USeq, CalculatePerCycleErrorRate, SamAlignmentExtractor, MergePairedAlignments
* Added option to export key QC metrics in json format
* Moved base summary stats to MergePairedAlignments to get a more accurate uniOb count for total, Q20, and Q30
MergeRegions
* Fixed issue of running this on java 1.7+ with contract sort violation
MpileupParser
* New App for parsing a SAMTools mpileup output file for non reference bases generating PointData for the reference, non reference, and fraction non reference for bases that pass the minimum read coverage filter.
Histogram
* Changed counters to use long instead of int to avoid overflow, this affects ~10 apps

----USeq_8.9.4----
SamAlignmentExtractor
* Rewrote the app to enable processing deep coverage datasets without exceeding memory requirements. Added lots of QC metrics.
BamBlaster
* New app for injecting snv and indel variants from a vcf file into a bam file
BamMixer
* New app for mixing BamBlaster alignments into different frequency tumor samples
VCFMutationMaker
* New app to generate vcf files with random snvs and indels over target regions for BamBlaster

Lots of mods related to filtering sam alignments for quality to deal with the NextSeq500 data. New features for the simulated tumor sample generation apps.

Made a variety of modifications to support a new app, BamMixer, that wraps a variety of useq apps to generate simulated somatic datasets. Adding in another new app, VCFVariantMaker that generates a vcf file of random snv and indels for use with the BamBlaster app.

Whole lot of mods and apps related to Bam QC, Extracting alignments, and calling CNVs. New app for injecting variants from a VCF file into bam alignments. Gave up fighting with BamSurgeon.

Finished CalculatePerCyclePerNucleotideErrorRate. It would be useful to extend this to looking for insertion/deletion errors by position as well, instead of simply providing counts for the number of reads with insertion/deletion events.

Sam2USeq: Fixed an issue where chromData from the MergePairedAlignments app fail to calc read coverage with b37 no "chr" data. Now must match the bed file with the alignments.

PoReCNV: change the way loaded data is saved to enable per sample loading for additional runs.

VCF mods to support parsing of LoFreq's crazy vcf format

New app for converting a bed file to a gene table by intersecting it with another gene table.

OK:
1) updating the .project file and the new way Eclipse creates faceted projects. Hopefully this minimize the hell of getting USeq installed in Eclipse
2) Added some mods to the CollectBamStats app to skip particular parsing if the log file doesn't have it
3) Added Z-Score calcs, graphs, and xls and bed output to PoReCNV to help in calling real CNVs