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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.

biotelerock 2015-06-06

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/cnv/PoReCNV.java
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/edu/utah/seq/vcf/VCFComments.java
changed /trunk/Source/edu/utah/seq/vcf/VCFComparator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFParser.java
added /trunk/Source/util/bio/annotation/Bed2UCSCRefFlat.java
changed /trunk/Source/util/bio/parsers/UCSCGeneLine.java
changed /trunk/build.properties
/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/cnv/PoReCNV.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFComments.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFComparator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFParser.java Diff Switch to side-by-side view
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/trunk/Source/util/bio/annotation/Bed2UCSCRefFlat.java Diff Switch to side-by-side view
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/trunk/Source/util/bio/parsers/UCSCGeneLine.java Diff Switch to side-by-side view
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/trunk/build.properties Diff Switch to side-by-side view
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