Commit [r1717] Maximize Restore History

Add support for reading, writing and on-the-fly creation of Tabix indices in tribble library. Now one can request on-the-fly indexing when using VariantContextWriterFactory to create a block-compressed VCF. In addition, lots of clean-up of the Tribble APIs.

alecw 2014-03-10

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added /trunk/src/java/net/sf/samtools/BinningIndexBuilder.java
added /trunk/src/java/net/sf/samtools/BinningIndexContent.java
added /trunk/src/java/net/sf/samtools/GenomicIndexUtil.java
changed /trunk/src/java/net/sf/samtools/AbstractBAMFileIndex.java
changed /trunk/src/java/net/sf/samtools/BAMIndexContent.java
changed /trunk/src/java/net/sf/samtools/BAMIndexer.java
changed /trunk/src/java/net/sf/samtools/Bin.java
changed /trunk/src/java/net/sf/samtools/BinaryBAMIndexWriter.java
changed /trunk/src/java/net/sf/samtools/CachingBAMFileIndex.java
changed /trunk/src/java/net/sf/samtools/Chunk.java
changed /trunk/src/java/net/sf/samtools/LinearIndex.java
changed /trunk/src/java/net/sf/samtools/SAMRecord.java
changed /trunk/src/java/net/sf/samtools/SAMUtils.java
changed /trunk/src/java/net/sf/samtools/TextualBAMIndexWriter.java
changed /trunk/src/java/net/sf/samtools/util/BlockCompressedInputStream.java
changed /trunk/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java
changed /trunk/src/java/org/broad/tribble/AbstractFeatureReader.java
changed /trunk/src/java/org/broad/tribble/AsciiFeatureCodec.java
changed /trunk/src/java/org/broad/tribble/BinaryFeatureCodec.java
changed /trunk/src/java/org/broad/tribble/FeatureCodec.java
changed /trunk/src/java/org/broad/tribble/index/AbstractIndex.java
changed /trunk/src/java/org/broad/tribble/index/Block.java
changed /trunk/src/java/org/broad/tribble/index/DynamicIndexCreator.java
changed /trunk/src/java/org/broad/tribble/index/Index.java
copied /trunk/src/java/org/broad/tribble/readers/LocationAware.java -> /trunk/src/java/net/sf/samtools/util/LocationAware.java
/trunk/src/java/net/sf/samtools/BinningIndexBuilder.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/BinningIndexContent.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/GenomicIndexUtil.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/AbstractBAMFileIndex.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/BAMIndexContent.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/BAMIndexer.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/Bin.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/BinaryBAMIndexWriter.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/CachingBAMFileIndex.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/Chunk.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/LinearIndex.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/SAMRecord.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/SAMUtils.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/TextualBAMIndexWriter.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/util/BlockCompressedInputStream.java Diff Switch to side-by-side view
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/trunk/src/java/net/sf/samtools/util/BlockCompressedOutputStream.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/AbstractFeatureReader.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/AsciiFeatureCodec.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/BinaryFeatureCodec.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/FeatureCodec.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/index/AbstractIndex.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/index/Block.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/index/DynamicIndexCreator.java Diff Switch to side-by-side view
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/trunk/src/java/org/broad/tribble/index/Index.java Diff Switch to side-by-side view
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