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gatk-3.8/java/src/org/broadinstitute/sting/utils
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ebanks 36fb6ca3c5 Allow user to specify the compression to be used when writing out BAM files. 
Updated most of the walkers to reflect this change.
Now it won't take forever to write BAMs!



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@909 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-06-05 08:48:34 +00:00
..
cmdLine Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments. 2009-06-02 22:41:10 +00:00
duplicates Revised ROD system. Split the system in Basic type and interface. Enabled more control over rod accessing, including an initialize() function to fetch headers and other options from the file. Added general tabular rod, which has a named columns and supports a map<String,String> interface. Comes with shiny new Junit system for RODs. Also, added simple python script for accessing picard data. 2009-05-14 21:06:28 +00:00
fasta Cleaned up error when fasta index is missing. Code still throws an exception, but the message is more direct (no more 'error while micromanaging') and tells the user to run 'samtools faidx' to fix the issue. 2009-06-01 15:34:38 +00:00
glf added some more documentation to the GLF writer and it's supporting classes, and some other fixes 2009-06-02 14:53:58 +00:00
io Lazy creation of output streams. Only create output streams when absolutely necessary. 2009-05-26 21:56:57 +00:00
sam We're no longer in the read-dropping business. 2009-06-04 22:37:51 +00:00
threading Break out some of the weird inner classes out of the HierachicalMicroScheduler. 2009-04-29 21:07:07 +00:00
windowmaker template for windowmaker utility -- total non-functional 2009-05-07 18:13:03 +00:00
BaseUtils.java fixing insidious bugs 2009-06-02 18:33:45 +00:00
BasicPileup.java Better accessors for dealing with second base prob pileups 2009-05-21 22:25:16 +00:00
ComparableSAMRecord.java We need to sort cleaned reads ourselves (instead of letting SAMFileWriter 2009-05-11 15:43:42 +00:00
FileProgressTracker.java moved a bunch of files over to the logging system. In some cases I ballparked the severity level of an error, so if you see something wrong feel free to make changes. 2009-03-27 14:02:55 +00:00
GenomeLoc.java slightly improved error message printed upon failure to parse interval list file 2009-06-04 18:24:43 +00:00
GenomeLocSortedSet.java Added back end code support for Sharding based on genomic location for reads. Changed the sharding 2009-05-26 20:57:46 +00:00
GenotypeUtils.java minor changes 2009-05-26 21:03:06 +00:00
JVMUtils.java intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails 2009-05-29 15:56:55 +00:00
LogisticRegressor.java Several changes to CovariateCounter walker to print more tables (called vs. observed Q scores), bug fixes to LogisticRecalibrationWalker and LogisticRegressor, and print string functionality added to Pair. 2009-04-28 00:37:48 +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 A better (less overflow-y) implementation of multinomialProbability(). 2009-05-01 06:28:16 +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 General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool. 2009-04-14 22:13:10 +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 Better accessors for dealing with second base prob pileups 2009-05-21 22:25:16 +00:00
ReadBackedPileup.java qualsAsInt argument for Pileup -- fixing stupid bug [again] 2009-06-04 18:52:12 +00:00
RefHanger.java Added convenience functions for RefHanger 2009-05-01 21:14:40 +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 Allow user to specify the compression to be used when writing out BAM files. 2009-06-05 08:48:34 +00:00
xReadLines.java Documentation and cleanup of xReadLines. 2009-03-25 15:36:21 +00:00