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Fixed an issue with the JavaxComOrgInfoNetClasses.zip archive, needed to update this to contain the latest Excel POI classes. More mods for H1K BamQC. This is complete now and ready to go. Fixed an issue with the VarScanVCFParser where it wasn't inserting the ssc score into the QUAL field.

biotelerock 2014-12-18

Browse code at this revision

Parent: [r278]

Child: [r280]

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Misc/JavaxComOrgInfoNetClasses.zip
added /trunk/Misc/JavaxComOrgInfoNetClassesOld.zip
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/edu/utah/seq/parsers/CollectBamStats.java
changed /trunk/Source/edu/utah/seq/vcf/VarScanVCFParser.java
changed /trunk/Source/util/gen/Email.java
added /trunk/Source/util/gen/Gmail.java
changed /trunk/build.properties
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/trunk/Misc/JavaxComOrgInfoNetClasses.zip
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/trunk/Misc/JavaxComOrgInfoNetClassesOld.zip
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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/parsers/CollectBamStats.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VarScanVCFParser.java Diff Switch to side-by-side view
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/trunk/Source/util/gen/Email.java Diff Switch to side-by-side view
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/trunk/Source/util/gen/Gmail.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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