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gatk-3.8/public/java/src/org/broadinstitute/sting/utils/sam
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Mark DePristo aa3ee29929 Handle case where the ReadGroup is null in GATKSAMRecord 2012-12-24 13:35:57 -05:00
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AlignmentStartComparator.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
AlignmentStartWithNoTiesComparator.java Fix subtle bug in the ReduceReads stash reported by Adam 2012-02-23 18:35:25 -05:00
AlignmentUtils.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
ArtificialMultiSampleReadStream.java Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
ArtificialPatternedSAMIterator.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArtificialReadsTraversal.java Refactor TraversalEngine to extract the progress meter functions 2012-09-10 20:14:13 -04:00
ArtificialSAMFileReader.java Downsampling: experimental engine integration 2012-09-06 15:03:27 -04:00
ArtificialSAMFileWriter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArtificialSAMIterator.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
ArtificialSAMQueryIterator.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
ArtificialSAMUtils.java Incorporating clover into build.xml 2012-12-24 13:35:57 -05:00
ArtificialSingleSampleReadStream.java Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
ArtificialSingleSampleReadStreamAnalyzer.java Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
BySampleSAMFileWriter.java Implementation of BySampleSAMFileWriter 2012-11-14 10:33:22 -05:00
ComparableSAMRecord.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
GATKSAMReadGroupRecord.java The GATK engine now ensures that incoming GATKSAMRecords have GATKSAMReadGroupRecord objects in their header 2012-12-24 13:35:09 -05:00
GATKSAMRecord.java Handle case where the ReadGroup is null in GATKSAMRecord 2012-12-24 13:35:57 -05:00
GATKSamRecordFactory.java Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs. 2011-10-21 09:59:24 -04:00
MisencodedBaseQualityReadTransformer.java Quick fix: base qual array in the GATKSAMRecord stores the actual phred values (-33) and not the original bytes (duh). 2012-12-03 12:18:20 -05:00
NWaySAMFileWriter.java Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters 2012-11-14 10:33:22 -05:00
ReadUnclippedStartWithNoTiesComparator.java New ReduceReads v2 with unclipped variant regions and soft-clipped bases 2012-06-08 14:58:31 -04:00
ReadUtils.java The GATK engine now ensures that incoming GATKSAMRecords have GATKSAMReadGroupRecord objects in their header 2012-12-24 13:35:09 -05:00
SAMFileReaderBuilder.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
SimplifyingSAMFileWriter.java Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00