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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.

biotelerock 2015-06-26

changed /trunk/Source/edu/utah/seq/data/SamSubsampler.java
changed /trunk/Source/edu/utah/seq/parsers/MergeSams.java
changed /trunk/Source/edu/utah/seq/parsers/SamAlignmentExtractor.java
changed /trunk/Source/edu/utah/seq/vcf/sim/BamBlaster.java
added /trunk/Source/edu/utah/seq/vcf/sim/BamMixer.java
added /trunk/Source/edu/utah/seq/vcf/sim/VCFVariantMaker.java
changed /trunk/Source/util/bio/annotation/Bed.java
changed /trunk/build.properties
/trunk/Source/edu/utah/seq/data/SamSubsampler.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/MergeSams.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/parsers/SamAlignmentExtractor.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/sim/BamBlaster.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/sim/BamMixer.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/sim/VCFVariantMaker.java Diff Switch to side-by-side view
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/trunk/Source/util/bio/annotation/Bed.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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