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Did a bunch of reorganization and merging of vcf related classes under edu/utah/seq/vcf

biotelerock 2013-03-19

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Parent: [r74]

Child: [r76]

changed /trunk/Documentation/USeqDocumentation/applications.html
changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
renamed /trunk/Source/edu/utah/seq/base/MultiSampleVCFFilter.java -> /trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
changed /trunk/Source/edu/utah/seq/base/VariantAlignment.java
renamed /trunk/Source/edu/utah/seq/parsers/MultiSampleVCFParser.java -> /trunk/Source/edu/utah/seq/vcf/VCFParser.java
renamed /trunk/Source/edu/utah/seq/parsers/MultiSampleVCFRecord.java -> /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
renamed /trunk/Source/edu/utah/seq/parsers/VCFLookUp.java -> /trunk/Source/edu/utah/seq/vcf/VCFLookUp.java
removed /trunk/Source/edu/utah/seq/parsers/VCFParser.java
removed /trunk/Source/edu/utah/seq/parsers/VCFRecord.java
renamed /trunk/Source/edu/utah/seq/parsers/VCFSample.java -> /trunk/Source/edu/utah/seq/vcf/VCFSample.java
renamed /trunk/Source/edu/utah/seq/parsers/VCFTabix.java -> /trunk/Source/edu/utah/seq/vcf/VCFTabix.java
added /trunk/Source/edu/utah/seq/vcf
changed /trunk/build.properties
/trunk/Documentation/USeqDocumentation/applications.html Diff Switch to side-by-side view
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/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/base/MultiSampleVCFFilter.java to /trunk/Source/edu/utah/seq/vcf/MultiSampleVCFFilter.java
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/trunk/Source/edu/utah/seq/base/VariantAlignment.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/MultiSampleVCFParser.java to /trunk/Source/edu/utah/seq/vcf/VCFParser.java
File was renamed.
/trunk/Source/edu/utah/seq/parsers/MultiSampleVCFRecord.java to /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
File was renamed.
/trunk/Source/edu/utah/seq/parsers/VCFLookUp.java to /trunk/Source/edu/utah/seq/vcf/VCFLookUp.java
File was renamed.
/trunk/Source/edu/utah/seq/parsers/VCFParser.java
File was removed.
/trunk/Source/edu/utah/seq/parsers/VCFRecord.java
File was removed.
/trunk/Source/edu/utah/seq/parsers/VCFSample.java to /trunk/Source/edu/utah/seq/vcf/VCFSample.java
File was renamed.
/trunk/Source/edu/utah/seq/parsers/VCFTabix.java to /trunk/Source/edu/utah/seq/vcf/VCFTabix.java
File was renamed.
/trunk/Source/edu/utah/seq/vcf
Directory.
/trunk/build.properties Diff Switch to side-by-side view
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