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Big refactoring of the molecular barcode consenus calling tools to utilize preprocesing with the FastqBarcodeTagger MatchMates followed by Consensus. This cut the time in 1/2 and memory requirements to < 30G. This is ready to go and stable.

biotelerock 2015-09-23

Browse code at this revision

Parent: [r306]

Child: [r308]

changed /trunk/Documentation/USeqDocumentation/releaseNotes.txt
changed /trunk/Source/edu/utah/seq/barcodes/BarcodeChromMerger.java
added /trunk/Source/edu/utah/seq/barcodes/BarcodeChunk.java
changed /trunk/Source/edu/utah/seq/barcodes/BarcodeClusterEngine.java
added /trunk/Source/edu/utah/seq/barcodes/BarcodeLoader.java
changed /trunk/Source/edu/utah/seq/barcodes/Consensus.java
changed /trunk/Source/edu/utah/seq/barcodes/ConsensusEngine.java
removed /trunk/Source/edu/utah/seq/barcodes/ConsensusEngineListsForBrendan.java
added /trunk/Source/edu/utah/seq/barcodes/MatchMates.java
removed /trunk/Source/edu/utah/seq/barcodes/OldBarcodeChromMerger.java
removed /trunk/Source/edu/utah/seq/barcodes/TestBarcodeClustering.java
changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/util/gen/IO.java
changed /trunk/build.properties
/trunk/Documentation/USeqDocumentation/releaseNotes.txt Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/BarcodeChromMerger.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/BarcodeChunk.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/BarcodeClusterEngine.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/BarcodeLoader.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/Consensus.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/ConsensusEngine.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/ConsensusEngineListsForBrendan.java
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/trunk/Source/edu/utah/seq/barcodes/MatchMates.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/barcodes/OldBarcodeChromMerger.java
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/trunk/Source/edu/utah/seq/barcodes/TestBarcodeClustering.java
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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/util/gen/IO.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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