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gatk-3.8/java/src/org/broadinstitute/sting/utils
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ebanks dfe7d69471 1. VCF: don't print slod if it's never set 
2. UG: don't print slod if lods are infinite (todo: figure out a good guess instead)
3. UG: if probF=0 for 2 alt alleles are both 0 (because of precision), use log values to discriminate



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2116 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-11-23 02:55:43 +00:00
..
bed GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
cmdLine adding error log reporting to the GATK, and a stream based output method for the argument collection 2009-10-28 19:56:05 +00:00
containers Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 2009-10-20 12:23:36 +00:00
duplicates Pileup cleanup; pooled caller v1 2009-11-18 17:03:48 +00:00
fasta Bumping version of Picard for firehose compatibility. 2009-10-16 19:38:56 +00:00
fastq Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity. 2009-09-03 17:20:16 +00:00
genotype 1. VCF: don't print slod if it's never set 2009-11-23 02:55:43 +00:00
io Deleting lots of code as part of my cleanup. More classes tagged for removal. Many more walkers have their days numbered. 2009-10-20 12:23:36 +00:00
sam cleanup of the traversal output code 2009-11-12 06:18:10 +00:00
threading Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
AlignmentUtils.java the life in the magical kingdom of fully spec-conforming SAM files would be so... magical. For now, however, there are plenty of ways to end up with inconsistent SAM records. For instance, a SAM file with missing header will result in SAM records with ref. name set, but getReferenceIndex() returning null. This, in turn, was tripping isReadUnmapped(). The method is now fixed, so that it suffices to have *either* reference name *or* reference index set for the read to be considered mapped (the flag is still checked) 2009-09-14 16:04:19 +00:00
BaseUtils.java charSeq2byteSeq -- convert a char[] to a byte[] for convenience 2009-10-27 21:52:23 +00:00
BasicPileup.java updates to the paper genotyper based on Mark's comments. There's still more work to do, including more testing. 2009-11-19 23:06:49 +00:00
ComparableSAMRecord.java only compare pair position for paired end reads 2009-07-08 04:07:08 +00:00
ExpandingArrayList.java Now uses expanding array list for coverage histograms. No hard limit on maximum depth now 2009-09-16 23:27:25 +00:00
GATKErrorReport.java comments for eric 2009-11-13 14:19:31 +00:00
GenomeLoc.java code cleanup and containsStartPosition function 2009-10-27 21:53:40 +00:00
GenomeLocParser.java Validates intervals against sequence dictionary header bounds. 2009-10-22 19:31:15 +00:00
GenomeLocSortedSet.java GSA-182: Adding support for BED interval files. 2009-10-06 02:45:31 +00:00
GenotypeUtils.java intermediate commit for some changes in the Variation system, so Eric can go ahead with his changes. Everything is pretty set, but the Variation interface could use a convenience method that joins all the alternate alleles. 2009-10-23 06:31:15 +00:00
JVMUtils.java Better integrate the @ArgumentCollection into the command-line argument parser. Walkers can now specify their own @ArgumentCollections. Also cleaned up a bit of the CommandLineProgram template method pattern to minimize duplicate code. 2009-09-29 22:23:19 +00:00
ListUtils.java Cosmetic change to list sampling functions: the typical usage of n and k were reversed. No change in functionality of the classes has been made and unit tests still pass. 2009-09-28 18:12:32 +00:00
MalformedGenomeLocException.java A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu 2009-06-02 18:14:46 +00:00
MathUtils.java Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated. 2009-11-16 02:41:20 +00:00
MergingIterator.java General purpose merging iterator implementation 2009-09-12 19:06:15 +00:00
PackageUtils.java New PackageUtils interferes with the packaging utility. Revert until Aaron and 2009-11-02 19:14:14 +00:00
Pair.java The building blocks for segmenting covariate counting data by read group. 2009-06-04 19:55:24 +00:00
PathUtils.java Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm. 2009-05-21 19:31:54 +00:00
Pileup.java Pileup cleanup; pooled caller v1 2009-11-18 17:03:48 +00:00
PluginManager.java Allow users to directly specify filters from the command-line, applicable to 2009-11-10 18:40:16 +00:00
Predicate.java Push core / playground lower into the tree. 2009-03-23 23:19:54 +00:00
PrimitivePair.java Push core / playground lower into the tree. 2009-03-23 23:19:54 +00:00
QualityUtils.java Support for original quality scores OQ flag. pQ flag in TableRecalibation to preserve quality scores below a threshold (defaulting to 5) 2009-08-28 14:14:21 +00:00
ReadBackedPileup.java Pileup cleanup; pooled caller v1 2009-11-18 17:03:48 +00:00
SWPairwiseAlignment.java -set indel cleaning walkers to be in core package 2009-07-24 05:23:29 +00:00
StingException.java Changed Sting exception from a base exception to a runtime exception. This makes it so you can throw it without the consumer having to check it, and hopefully people will be more inclined to use it. 2009-04-29 22:09:41 +00:00
Utils.java a convenience method to join a map into a single string, which I need for some VCF work. Added some documentation to the join method as well. 2009-11-17 16:50:01 +00:00
package.html Package level documentation -- helps new users get acclimated to the codebase more quickly. 2009-06-17 16:27:48 +00:00
xReadLines.java Documentation and cleanup of xReadLines. 2009-03-25 15:36:21 +00:00