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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Eric Banks 58424e56be Setting the reduce reads count tag was all wrong in a previous commit; fixing. 
RR counts are represented as offsets from the first count, but that wasn't being done
correctly when counts are adjusted on the fly.  Also, we were triggering the expensive
conversion and writing to binary tags even when we weren't going to write the read
to disk.

The code has been updated so that unconverted counts are passed to the GATKSAMRecord
and it knows how to encode the tag correctly.  Also, there are now methods to write
to the reduced counts array without forcing the conversion (and methods that do force
the conversion).

Also:
1. counts are now maintained as ints whenever possible.  Only the GATKSAMRecord knows
about the internal encoding.
2. as discussed in meetings today, we updated the encoding so that it can now handle
a range of values that extends to 255 instead of 127 (and is backwards compatible).
3. tests have been moved from SyntheticReadUnitTest to GATKSAMRecordUnitTest accordingly.
 		2013-04-30 13:45:42 -04:00
..
R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
clipping Setting the reduce reads count tag was all wrong in a previous commit; fixing. 2013-04-30 13:45:42 -04:00
codecs/hapmap Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
collections Fixing license on Yossi's file 2013-02-05 11:14:43 -05:00
crypt Update MD5s to reflect version number change in the BAM header 2013-02-01 13:51:31 -05:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
file Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
fragments Bugfix for FragmentUtils.mergeOverlappingPairedFragments 2013-04-25 11:11:15 -04:00
haplotype Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
interval Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator LIBS unit test debugging should be false 2013-04-08 12:47:47 -04:00
nanoScheduler Further tweaking of test timeouts 2013-03-15 14:49:21 -04:00
pileup Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
progressmeter Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -05:00
recalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Setting the reduce reads count tag was all wrong in a previous commit; fixing. 2013-04-30 13:45:42 -04:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant AssessNA12878 bugfixes 2013-03-18 15:48:08 -04:00
AutoFormattingTimeUnitTest.java AutoFormattingTimeUnitTest should be in utils 2013-01-30 09:47:47 -05:00
BaseUtilsUnitTest.java More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -05:00
BitSetUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParserBenchmark.java Optimize GenomeLocParser.createGenomeLoc 2013-01-30 09:47:47 -05:00
GenomeLocParserUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
GenomeLocSortedSetUnitTest.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
GenomeLocUnitTest.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
MRUCachingSAMSequencingDictionaryUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
MWUnitTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtilsUnitTest.java Refactored binomial probability code in MathUtils. 2013-04-16 18:19:07 -04:00
MedianUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatformUnitTest.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtilsUnitTest.java Final edge case bug fixes to QualityUtil routines 2013-02-16 07:31:38 -08:00
SequenceDictionaryUtilsUnitTest.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimerUnitTest.java Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
UtilsUnitTest.java Cleanup of FragmentUtils 2013-03-13 07:36:20 -04:00