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  • ad63633b1c forgot to change the chunks dir to shards before aaron 2009-03-31 20:28:20 +0000
  • ede52f7359 - take command line arguments - output GFF lines to a file (specified by a command line argument) - improve the GFF output string jmaguire 2009-03-31 18:43:00 +0000
  • 8d601a6a42 unbox ebanks 2009-03-31 15:51:59 +0000
  • d37d81822d Fixed the Hello, World doc to reflect the collapse in the walker hierarchy. hanna 2009-03-31 15:23:29 +0000
  • 8e2ba7a294 Added more detail to documentation based on the feedback I've been getting on command-line arguments. hanna 2009-03-31 15:21:05 +0000
  • 234137dee8 use boolean instead of String for flag to suppress printing in map ebanks 2009-03-31 15:14:00 +0000
  • 907c183242 update walkers so that onTraversalDone works (it now takes an arg) ebanks 2009-03-31 15:05:33 +0000
  • 3896cc8f17 Moved avg depth of coverage functionality into the core depth of coverage walker. Used new command line args for walkers. ebanks 2009-03-31 05:02:33 +0000
  • 007ecc8616 Added a stateless walker to give the average depth of coverage for given reads ebanks 2009-03-31 02:33:59 +0000
  • 89c1762aa9 Apparently, no one else has tried to create a stateless walker over loci until now, as this should have come up: make sure reduce sums get transferred to the next reduce. ebanks 2009-03-31 02:31:51 +0000
  • ba99e9f648 checking in some of the more static Data Source dependent code at this point. They don't do much on their own, but are need for the base data source code I'm writing. aaron 2009-03-31 00:04:03 +0000
  • 7fda409f4e Fixed bug where read traversals would fail with an exception when not called with a genome_region (-L) argument. From TraversalEngine, line 455, looks like Mark intended an invariant where the list of locations is 0 length if not specified. Made GenomeLoc code compliant with that. hanna 2009-03-30 23:43:12 +0000
  • e812cfbf55 Refactor common functionality out of WalkerManager and into JVMUtils and PathUtils. Add support for loading walkers from a jar. hanna 2009-03-30 23:20:55 +0000
  • 8be02f6a34 Check in the omniplan file for easier sharing. hanna 2009-03-30 21:31:54 +0000
  • 20e650f397 Added examples that can be cut and pasted. hanna 2009-03-30 19:05:44 +0000
  • 36f851362e Oops. While writing command-line argument docs, I realized I introduced a regression in default value handling. hanna 2009-03-30 18:51:39 +0000
  • 875802e8fc print output as a GFF line. jmaguire 2009-03-30 17:47:35 +0000
  • b752960586 rearranged some stuff and eliminated the binomial prior in the N!=2 case. Much faster. jmaguire 2009-03-30 17:26:05 +0000
  • 1d972969a9 A dumping ground for information that will eventually become the GATK user manual. Currently has basic information about command-line arguments and walker output streams. hanna 2009-03-30 16:04:30 +0000
  • 7c6455fe36 Handle the case where a walker is being run outside of the GATK framework, such as JUnit tests. hanna 2009-03-29 01:50:27 +0000
  • cb6a3b7e55 Bug fix: build couldn't be forced to core. Now it can be. hanna 2009-03-29 01:36:25 +0000
  • c4f0b4cab7 Oops. Javadoc output gets a lot cleaner when I remember to add the classpath. hanna 2009-03-29 00:29:20 +0000
  • 74cae62ac2 Cleaned up generation of javadoc code. Still need to fix javadoc generation to take external dependencies into account. hanna 2009-03-29 00:03:08 +0000
  • d7c0bcc223 Reorganized GenomeLoc code to more clearly and better use the picard SequenceDictionary information. All GenomeLoc[] are not ArrayList<GenomeLoc> for clarity and consistency Parsing now recursively merges contiguous elements chr1:1-10;chr1:11-20 => chr1:1-20 Added support for TraversingByLoci over all reference positions specified by the provided location array. System dynamically determines which traversal system to use. Pileup now marks, very clearly, reference positions without covered reads. Made changes around the codebase to deal with new GenomeLoc structure. depristo 2009-03-28 20:37:27 +0000
  • c2ae6765a3 Removed unnecessary dependence on playground code... depristo 2009-03-27 22:48:51 +0000
  • fade36a8f2 Add targets to force build to core and force build to playground. hanna 2009-03-27 22:32:44 +0000
  • b17a03abbd Fix argument parser test case. hanna 2009-03-27 16:05:18 +0000
  • cfee59e0e6 New type hierarchy for Traversals. There's a new package to hold them (traversals) and an easy system to create new ones. We are now one step closer to supporting the execution manager (a totally non-functional version is included here) that actually executes walkers in parallel using N threads. depristo 2009-03-27 15:40:45 +0000
  • 4a6be896b9 Provide out and err PrintStreams to the walkers. hanna 2009-03-27 15:03:32 +0000
  • c6d9848d08 synchronizing latest changes asivache 2009-03-27 14:15:44 +0000
  • 230c1ad161 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. aaron 2009-03-27 14:02:55 +0000
  • 826781a760 The traversal engine now passes the reduce result to OnTraversalDone() in the walker base class depristo 2009-03-27 13:44:46 +0000
  • d115209e86 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. aaron 2009-03-27 13:27:04 +0000
  • 935a4d81c9 fixed the problem where you could specify a logging level that didn't exist aaron 2009-03-27 04:29:27 +0000
  • 067ae09cd0 Bump picard and samtools to latest. hanna 2009-03-27 02:26:28 +0000
  • 3abaaa3cc3 Tried to add a poor man's version of seeing all reference sites in an interval, and failed. However, I did add the command line argument and a few pieces of useful code. depristo 2009-03-27 00:12:35 +0000
  • f7097c8ee7 Cleanup. hanna 2009-03-26 21:24:12 +0000
  • 728f932ecf Fix exclusive options. hanna 2009-03-26 20:59:32 +0000
  • 53fe9acf65 Make command-line arguments available in walker constructor, provide back door from walker into GATK itself, do some cleanup of output messages, and add some bug fixes. Command-line arguments in walkers are now feature-complete, but still a bit messy. hanna 2009-03-26 20:45:27 +0000
  • 1d95f06ad5 Fix path issue generating javadocs. hanna 2009-03-26 18:51:56 +0000
  • 5f9010116a Collapse the walker hierarchy, in preparation for in-walker output streams less hokey walker args. hanna 2009-03-26 16:22:35 +0000
  • 7cad3acc61 Support for dynamically merging data files. Preliminary only -- everything in these systems is still being tested depristo 2009-03-26 14:40:50 +0000
  • 2808fd4bbd Better support for required mutually exclusive options. hanna 2009-03-26 03:22:30 +0000
  • 08ece8df79 Bug fixes and support for mutually exclusive options. Still a bit rough, but will be easier to clean up after a walker refactoring. hanna 2009-03-26 03:11:56 +0000
  • f47a214f96 massive changes everywhere; lots of bugs fixed; methods moved around; computation and printout of overall stats added; now decides whether to accept or reject 'improvement'; writes alignments into two output sam files (unmodified reads/failed piles into one, realigned piles into the other); special treat for paranoids: writes third sam file with all the analyzed reads, unmodified asivache 2009-03-26 02:26:17 +0000
  • 0331cd8e95 Updated AlleleFrequency* classes to calculate separate lods for VarVsRef and BestVsNextBest mixture (qstar) theories; AFWMetrics now reports single sample performance w.r.t. Hapmap chip using the appropriate lod for gentoyping (BestVsNextBest) or variant / reference calling (VarVsRef). andrewk 2009-03-26 02:10:18 +0000
  • c88a17dfee AlleleFrequencyWalker now can parse 4-base probs andrewk 2009-03-25 20:33:05 +0000
  • 4b7bfb284a Support for more complex command-line types: arrays, untyped collections, typed collections, interfaces to typed and untyped collections. hanna 2009-03-25 20:11:31 +0000
  • 9840a089ef Added documentation for our coding standards. aaron 2009-03-25 19:42:09 +0000
  • 2ed63fe17c a bunch of changes that support pools. jmaguire 2009-03-25 18:52:42 +0000
  • d457778283 Unified byLoci and byLociByInterval traversals. It now figures out what to do for you based on the presence of an index and set of required locations to process. depristo 2009-03-25 16:01:58 +0000
  • c18f8fbf5f Documentation and cleanup of xReadLines. depristo 2009-03-25 15:36:21 +0000
  • 607731da91 Fixed a harmless (but annoying) bug wherein the read name for the SAMRecords increases by two on every iteration rather than one. kiran 2009-03-25 15:20:29 +0000
  • 44acc358b7 Add a "notes" member to the AlleleFreqencyEstimate, e.g. for hapmap metadata. jmaguire 2009-03-25 15:18:10 +0000
  • d11bb0fc64 Added xReadLines class to utils. It is a iterator<string> and iterable<string> so you can easily read all lines from a file. It's been used to simplify the code to process intervals, and will be used to add merging data support to the system... depristo 2009-03-25 15:17:38 +0000
  • 4c29dca70d git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@186 348d0f76-0448-11de-a6fe-93d51630548a asivache 2009-03-25 09:23:42 +0000
  • 71d3e8e99b fixed another bug in gapped alignment computation asivache 2009-03-25 08:33:57 +0000
  • 40f45c2333 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@184 348d0f76-0448-11de-a6fe-93d51630548a asivache 2009-03-25 05:48:10 +0000
  • 8bdf49a01f added slightly more useful output to Depth of Coverage walker. (now prints number of loci). Traversal engine now actually prints the reduce result (key) and no longer prints millions of locus interval updates depristo 2009-03-25 03:12:54 +0000
  • ff98e28abf High-performance interval list implement -- uses StringBuilder to avoid n^2 calculation. Can handle millions of locations quickly now depristo 2009-03-25 02:17:48 +0000
  • 30babbf5b9 Restructured AlleleFrequencyMetricsWalker to correctly report Hapmap concordance numbers for genotyping and added reporting for Hapmap reference/variant calling. Also, tiny bugfix in interval code. andrewk 2009-03-25 01:12:05 +0000
  • 9e2a373184 Prototype, buggy implementation of walker command-line arguments. Doesn't (yet) deal elegantly with even simple cases. hanna 2009-03-25 00:12:00 +0000
  • 919a86e876 Cleaned up code for by interval traversals for Jared. Initialization code refactored and made clear. by loci and by loci by interval use the same underlying code now. Everyone uses the same initialization code to set things up. It's a party in the TraversalEngine and everyone's invited... depristo 2009-03-24 22:32:45 +0000
  • 28c1330b4b Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined). kiran 2009-03-24 21:59:25 +0000
  • c047b53d6b added some cleanup of code, and new junit targets to the build file aaron 2009-03-24 21:16:12 +0000
  • c2b2ed8e1d added our first junit test, for the argument parser aaron 2009-03-24 21:14:30 +0000
  • 6df19ab793 Support for byInterval traversals for Jared. Do not use them. depristo 2009-03-24 20:55:34 +0000
  • 9f500215da Support for reseting the system; Cleanup later depristo 2009-03-24 20:52:11 +0000
  • 499c422de6 A version of the four-base caller that computes the probability distribution over base call space by initializing off the Bustard calls rather than the ICs. kiran 2009-03-24 20:11:39 +0000
  • a55d630ef9 Added FourBaseRecaller to list of jar targets (this is just until I figure out the appropriate way to combine FourBaseCaller and FourBaseRecaller). kiran 2009-03-24 20:10:48 +0000
  • 4222016bf5 stop printing sw matrix and other debug infoant asivache 2009-03-24 18:15:52 +0000
  • 8ea8a74fbf fixed bug in calculation of alignment start offset for negative offsets; toString() added asivache 2009-03-24 18:05:28 +0000
  • 9aa1ccd9b7 fixed some bugs in calling the optimal path; parameters adjusted (?) asivache 2009-03-24 17:27:51 +0000
  • 88d94d407a Fixed a bug in the parsing of the second end of the pair. kiran 2009-03-24 14:34:37 +0000
  • 786a7845dd git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@167 348d0f76-0448-11de-a6fe-93d51630548a asivache 2009-03-24 14:06:44 +0000
  • 3d1e0bf079 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@166 348d0f76-0448-11de-a6fe-93d51630548a asivache 2009-03-24 14:06:24 +0000
  • a3b8830855 need more access, found out in junit testing aaron 2009-03-24 13:22:09 +0000
  • 908065125f computes Smith-Waterman pairwise alignment asivache 2009-03-24 05:36:37 +0000
  • 9dee9ab51c Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter. andrewk 2009-03-24 03:58:03 +0000
  • f7363cf935 Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging. hanna 2009-03-24 03:56:49 +0000
  • ff5b0ec1b6 Get rid of playground and core root directories. hanna 2009-03-23 23:26:05 +0000
  • 63cd1fe201 Push core / playground lower into the tree. hanna 2009-03-23 23:19:54 +0000
  • c5bd4a1af4 made the class that we pull fields from of type Object, so we can use any class (that has the specified fields). aaron 2009-03-23 21:04:11 +0000
  • 741dd357de typo aaron 2009-03-23 20:51:01 +0000
  • b56a73538d add all the input in Traversal Engine over to the logging engine aaron 2009-03-23 20:46:55 +0000
  • d174417fbd added some logger calls instead of the warn / scare user calls. aaron 2009-03-23 20:27:21 +0000
  • 5cdc5dffc6 Added some code to handle pairs properly, extend IC solution beyond IC reference length, and allow output to a specified file. kiran 2009-03-23 19:42:31 +0000
  • 2ee2623926 Move non-java code out of playground. hanna 2009-03-23 19:31:38 +0000
  • 8efcb6a3b4 We now just warn about extra parameters, and provide more information if we fail to convert a command line parameter to the specified type from a string. aaron 2009-03-23 19:03:59 +0000
  • 27353af216 Matt pointed out that some long names were capitalized and some were not, and that's just plain uncool; to which I agreed. Now that's fixed. aaron 2009-03-23 15:01:32 +0000
  • 08ca2ce89b fixing accidental incomplete commit asivache 2009-03-23 14:39:15 +0000
  • 2dd14d7c17 auxiliary class for SequencePile, just one column of the MSA asivache 2009-03-23 14:37:49 +0000
  • 29136ee892 Arachne's alignment pile, more or less. Can accept sequences with alignments (cigars) and generate nice alignment pile plot with indels asivache 2009-03-23 14:36:00 +0000
  • 0188379174 PrimitivePair.\* : pair(s) based directly on primitive types. Hail generics. asivache 2009-03-23 14:12:22 +0000
  • 1f60c70688 Missing STL. Added Pair<X,Y> asivache 2009-03-23 14:04:16 +0000
  • 835e85374e git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@146 348d0f76-0448-11de-a6fe-93d51630548a asivache 2009-03-23 05:46:09 +0000
  • 046cecb067 Switched our code over to the new command line style (gnu style args), added the initial logger code, and added apache commons CLI to the IVY script. aaron 2009-03-22 21:06:22 +0000
  • 38f18c8679 added generic SortPermutation that returns sorting permutation for arbitrary List<T> as long as T is Comparable asivache 2009-03-22 20:40:26 +0000
  • 09d605bb37 Changed how the example walker gets run, I'm about to check in the GNU style command line args. aaron 2009-03-22 20:10:17 +0000
  • 02556ce4a6 Moved to core depristo 2009-03-22 20:02:19 +0000