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cmdLine
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Eric wins the prize for pointing out that doubles weren't valid command-line arguments. Made all primitive types parseable as command-line arguments.
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2009-06-02 22:41:10 +00:00 |
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duplicates
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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.
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2009-05-14 21:06:28 +00:00 |
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fasta
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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.
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2009-06-01 15:34:38 +00:00 |
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glf
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added some more documentation to the GLF writer and it's supporting classes, and some other fixes
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2009-06-02 14:53:58 +00:00 |
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io
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Lazy creation of output streams. Only create output streams when absolutely necessary.
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2009-05-26 21:56:57 +00:00 |
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sam
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added tools to test read based traversals using the artificial in-memory SAM file tools, and testing of the PrintReadsWalker
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2009-06-10 01:52:25 +00:00 |
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threading
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Break out some of the weird inner classes out of the HierachicalMicroScheduler.
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2009-04-29 21:07:07 +00:00 |
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windowmaker
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template for windowmaker utility -- total non-functional
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2009-05-07 18:13:03 +00:00 |
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BaseUtils.java
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Added some methods to generate random bases or random base indexes, optionally disallowing the generation of a specified base or base index.
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2009-06-09 00:47:54 +00:00 |
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BasicPileup.java
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Better accessors for dealing with second base prob pileups
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2009-05-21 22:25:16 +00:00 |
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ComparableSAMRecord.java
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We need to sort cleaned reads ourselves (instead of letting SAMFileWriter
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2009-05-11 15:43:42 +00:00 |
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FileProgressTracker.java
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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.
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2009-03-27 14:02:55 +00:00 |
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GenomeLoc.java
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added hashCode()
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2009-06-08 16:52:02 +00:00 |
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GenomeLocSortedSet.java
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Added back end code support for Sharding based on genomic location for reads. Changed the sharding
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2009-05-26 20:57:46 +00:00 |
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GenotypeUtils.java
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minor changes
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2009-05-26 21:03:06 +00:00 |
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JVMUtils.java
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intercept NullPointerException and rethrow it with (marginally) comprehensible error message when an attempt to get class source code location fails
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2009-05-29 15:56:55 +00:00 |
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LogisticRegressor.java
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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.
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2009-04-28 00:37:48 +00:00 |
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MalformedGenomeLocException.java
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A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu
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2009-06-02 18:14:46 +00:00 |
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MathUtils.java
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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2009-06-05 23:34:37 +00:00 |
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Pair.java
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The building blocks for segmenting covariate counting data by read group.
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2009-06-04 19:55:24 +00:00 |
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PathUtils.java
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Added a method to refresh an NFS mount point (necessary to prevent NFS flakiness when running on the LSF farm.
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2009-05-21 19:31:54 +00:00 |
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Pileup.java
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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.
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2009-04-14 22:13:10 +00:00 |
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Predicate.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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PrimitivePair.java
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Push core / playground lower into the tree.
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2009-03-23 23:19:54 +00:00 |
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QualityUtils.java
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Better accessors for dealing with second base prob pileups
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2009-05-21 22:25:16 +00:00 |
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ReadBackedPileup.java
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qualsAsInt argument for Pileup -- fixing stupid bug [again]
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2009-06-04 18:52:12 +00:00 |
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RefHanger.java
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Added convenience functions for RefHanger
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2009-05-01 21:14:40 +00:00 |
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StingException.java
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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.
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2009-04-29 22:09:41 +00:00 |
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Utils.java
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
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2009-06-05 23:34:37 +00:00 |
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xReadLines.java
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Documentation and cleanup of xReadLines.
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2009-03-25 15:36:21 +00:00 |
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