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gatk-3.8/java/src/org/broadinstitute/sting/utils
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bthomas 5b34bb9ab0 Adding three minor new features: 
+ -L all now walks over all intervals

+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.

+ Error is thrown if the start position on an interval is higher number than the end position.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3021 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-17 16:24:10 +00:00
..
bed Looks bigger than it is: 2010-01-15 00:14:35 +00:00
cmdLine Update our error messages to point to getsatisfaction.com/gsa. 2010-01-27 19:16:28 +00:00
duplicates Removed used routines in duputils; duplicatequals to archive; docs for new duplicate traversal code; general code cleanup; bug fixes for combineduplicates; integration tests for combine duplicates walker 2009-12-29 19:46:29 +00:00
fasta Put a major.minor version into the GATK Javadoc for reading. Also, 2010-01-15 21:48:30 +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 Fix for Kiran: -1 is a valid value for genotype qualities in VCF, so VariantContext shouldn't die. Cleaned up the relevant VCF code while I was in there. 2010-03-17 00:20:15 +00:00
help Basic support for very simple index-driven locus traversals. Interface has been changed to 2010-01-29 03:14:26 +00:00
pileup new method to filter out overlapping PE reads 2010-03-15 15:40:09 +00:00
sam -Pushed base quals back down into SAMRecord; if -OQ is used, the SAMRecord quals get updated automatically 2010-03-17 16:00:10 +00:00
threading Put a major.minor version into the GATK Javadoc for reading. Also, 2010-01-15 21:48:30 +00:00
AlignmentUtils.java refactored to provide a sum of mismatch quality scores capability as well (used by Cancer) 2010-03-02 16:40:03 +00:00
BaseUtils.java Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP 2010-03-14 21:08:14 +00:00
CircularArray.java More archiving (with permission from Andrey) plus a move to core. 2009-12-03 15:40:27 +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 Looks bigger than it is: 2010-01-15 00:14:35 +00:00
GenomeLoc.java code cleanup and containsStartPosition function 2009-10-27 21:53:40 +00:00
GenomeLocParser.java Adding three minor new features: 2010-03-17 16:24:10 +00:00
GenomeLocSortedSet.java Unit tests for -XL arguments; expt. annotation calculating the GC content within 100 bp of the current SNP 2010-03-14 21:08:14 +00:00
JVMUtils.java Refactor the code I gave Eric yesterday to output command line arguments. 2009-12-10 18:57:54 +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 Added - new tests (Hapmap was re-added) 2009-12-14 21:57:20 +00:00
MergingIterator.java some rods-for-reads cleaning and performance improvements. 2010-03-10 22:54:58 +00:00
NestedHashMap.java Optimization - Added method to Covariates: void getValues( SAMRecord read, Comparable[] comparable ) which takes an array of size (at least) read.getReadLength() and fills it with covariate values for all positions in the given read. Made CovariateCounterWalker and TableRecalibrationWalker use this method instead of calling getValue(..) for each covariate and each offset. 2010-02-22 17:35:25 +00:00
PackageUtils.java Removing an accidently added import statement. 2010-02-10 15:54:24 +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
PluginManager.java a start to some of the infrastructure for Tribble, including dynamic detection of new RMD; not nearly wired in or complete yet. 2010-02-18 18:43:52 +00:00
PrimitivePair.java added PrimitivePair.Long and a few shortcut utility methods to PrimitivePairs: add(pair), subtract(pair), assignFrom(pair) 2009-12-14 00:15:44 +00:00
QualityUtils.java Modifications: 2010-01-06 19:18:07 +00:00
SWPairwiseAlignment.java - Change sortOnDisk option to sortInMemory 2010-02-17 20:52:57 +00:00
SampleUtils.java Moving UnifiedGenotyper and VariantAnnotator over to VariantContext system. 2010-03-09 03:41:07 +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
TextFormattingUtils.java Better handling of enums by the command-line argument system. 2010-01-20 21:36:46 +00:00
Utils.java VariantContext to VCF converter. BeagleROD, and phasing of VCF calls. Integration tests galore :-) 2010-02-09 19:02:25 +00:00
WilcoxonRankSum.java Get rid of characters in the docs that aren't universally compatible with 2009-12-07 21:41:07 +00:00
package-info.java Put a major.minor version into the GATK Javadoc for reading. Also, 2010-01-15 21:48:30 +00:00
xReadLines.java Documentation and cleanup of xReadLines. 2009-03-25 15:36:21 +00:00