USeq Source Code

Brought to you by: biotelerock, bmilash, elainegee, scourdy, tmosbruger

Commit [r305] Maximize Restore History

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.

Authored by: biotelerock 2015-08-05

Browse code at this revision

Parent: [r304]

Child: [r306]

changed	/trunk/Documentation/USeqDocumentation/releaseNotes.txt
removed	/trunk/Source/edu/utah/seq/compression/CompressFasta.java
changed	/trunk/Source/edu/utah/seq/data/Sam2USeq.java
added	/trunk/Source/edu/utah/seq/parsers/FastqBarcodeTagger.java
changed	/trunk/Source/edu/utah/seq/parsers/MpileupParser.java
changed	/trunk/Source/edu/utah/seq/useq/apps/Bar2USeq.java
changed	/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
added	/trunk/Source/edu/utah/seq/vcf/VCF2Bed.java
changed	/trunk/Source/edu/utah/seq/vcf/VCFSample.java
changed	/trunk/Source/trans/anno/GenomicRegion.java
changed	/trunk/Source/trans/anno/GenomicRegionComparator.java
changed	/trunk/Source/util/bio/annotation/Bed.java
changed	/trunk/build.properties

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/compression/CompressFasta.java

File was removed.

USeq Source Code

Commit [r305] Maximize Restore History

/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/compression/CompressFasta.java

/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/FastqBarcodeTagger.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/parsers/MpileupParser.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/useq/apps/Bar2USeq.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCF2Bed.java Diff Switch to side-by-side view

/trunk/Source/edu/utah/seq/vcf/VCFSample.java Diff Switch to side-by-side view

/trunk/Source/trans/anno/GenomicRegion.java Diff Switch to side-by-side view

/trunk/Source/trans/anno/GenomicRegionComparator.java Diff Switch to side-by-side view

/trunk/Source/util/bio/annotation/Bed.java Diff Switch to side-by-side view

/trunk/build.properties Diff Switch to side-by-side view