Commit [r2310] Maximize Restore History

Added code to CoverageMapBuilders to have extra option for maxCoverage to also for a min coverage requirement so some regions may go over maxCoverage if the read provides enough min coverage elsewhere.

dkatzel 2014-05-09

added /trunk/test/org/jcvi/jillion/assembly/util/TestCoverageMapBuilderMinCoverage.java
changed /trunk/src/org/jcvi/jillion/assembly/util/AbstractCoverageMapBuilder.java
changed /trunk/src/org/jcvi/jillion/assembly/util/ContigCoverageMapBuilder.java
changed /trunk/src/org/jcvi/jillion/assembly/util/CoverageMapBuilder.java
changed /trunk/src/org/jcvi/jillion/assembly/util/CoverageMapFactory.java
changed /trunk/src/org/jcvi/jillion/assembly/util/CoverageRegionBuilder.java
changed /trunk/src/org/jcvi/jillion/assembly/util/DefaultCoverageRegion.java
changed /trunk/test/org/jcvi/jillion/assembly/util/AllCoverageUnitTests.java
changed /trunk/test/org/jcvi/jillion/assembly/util/TestDefaultCoverageRegion.java
/trunk/test/org/jcvi/jillion/assembly/util/TestCoverageMapBuilderMinCoverage.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/AbstractCoverageMapBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/ContigCoverageMapBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/CoverageMapBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/CoverageMapFactory.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/CoverageRegionBuilder.java Diff Switch to side-by-side view
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/trunk/src/org/jcvi/jillion/assembly/util/DefaultCoverageRegion.java Diff Switch to side-by-side view
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/trunk/test/org/jcvi/jillion/assembly/util/AllCoverageUnitTests.java Diff Switch to side-by-side view
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/trunk/test/org/jcvi/jillion/assembly/util/TestDefaultCoverageRegion.java Diff Switch to side-by-side view
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