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170 Commits (c2b2ed8e1da479e35d1570eaf792b3506806a711)

Author SHA1 Message Date
aaron c2b2ed8e1d added our first junit test, for the argument parser 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@176 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 21:14:30 +00:00
depristo 6df19ab793 Support for byInterval traversals for Jared. Do not use them. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@175 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 20:55:34 +00:00
depristo 9f500215da Support for reseting the system; Cleanup later 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@174 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 20:52:11 +00:00
kiran 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@173 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 20:11:39 +00:00
kiran a55d630ef9 Added FourBaseRecaller to list of jar targets (this is just until I figure out the appropriate way to combine FourBaseCaller and FourBaseRecaller). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@172 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 20:10:48 +00:00
asivache 4222016bf5 stop printing sw matrix and other debug infoant 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@171 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 18:15:52 +00:00
asivache 8ea8a74fbf fixed bug in calculation of alignment start offset for negative offsets; toString() added 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@170 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 18:05:28 +00:00
asivache 9aa1ccd9b7 fixed some bugs in calling the optimal path; parameters adjusted (?) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@169 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 17:27:51 +00:00
kiran 88d94d407a Fixed a bug in the parsing of the second end of the pair. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@168 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 14:34:37 +00:00
asivache 786a7845dd git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@167 348d0f76-0448-11de-a6fe-93d51630548a 2009-03-24 14:06:44 +00:00
asivache 3d1e0bf079 git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@166 348d0f76-0448-11de-a6fe-93d51630548a 2009-03-24 14:06:24 +00:00
aaron a3b8830855 need more access, found out in junit testing 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@165 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 13:22:09 +00:00
asivache 908065125f computes Smith-Waterman pairwise alignment 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@164 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 05:36:37 +00:00
andrewk 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@163 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 03:58:03 +00:00
hanna f7363cf935 Support for loading from either a jar or a class directory. Fixes troubles with IntelliJ debugging. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@162 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-24 03:56:49 +00:00
hanna ff5b0ec1b6 Get rid of playground and core root directories. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@161 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 23:26:05 +00:00
hanna 63cd1fe201 Push core / playground lower into the tree. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@160 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 23:19:54 +00:00
aaron c5bd4a1af4 made the class that we pull fields from of type Object, so we can use any class (that has the specified fields). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@159 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 21:04:11 +00:00
aaron 741dd357de typo 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@158 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 20:51:01 +00:00
aaron b56a73538d add all the input in Traversal Engine over to the logging engine 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@157 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 20:46:55 +00:00
aaron d174417fbd added some logger calls instead of the warn / scare user calls. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@156 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 20:27:21 +00:00
kiran 5cdc5dffc6 Added some code to handle pairs properly, extend IC solution beyond IC reference length, and allow output to a specified file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@155 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 19:42:31 +00:00
hanna 2ee2623926 Move non-java code out of playground. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@154 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 19:31:38 +00:00
aaron 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@153 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 19:03:59 +00:00
aaron 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. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@152 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 15:01:32 +00:00
asivache 08ca2ce89b fixing accidental incomplete commit 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@151 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 14:39:15 +00:00
asivache 2dd14d7c17 auxiliary class for SequencePile, just one column of the MSA 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@150 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 14:37:49 +00:00
asivache 29136ee892 Arachne's alignment pile, more or less. Can accept sequences with alignments (cigars) and generate nice alignment pile plot with indels 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@149 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 14:36:00 +00:00
asivache 0188379174 PrimitivePair.\* : pair(s) based directly on primitive types. Hail generics. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@148 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 14:12:22 +00:00
asivache 1f60c70688 Missing STL. Added Pair<X,Y> 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@147 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-23 14:04:16 +00:00
asivache 835e85374e git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@146 348d0f76-0448-11de-a6fe-93d51630548a 2009-03-23 05:46:09 +00:00
aaron 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. 
There will be a slow conversion of all the System.out and System.err in other files to the logger style output.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@145 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 21:06:22 +00:00
asivache 38f18c8679 added generic SortPermutation that returns sorting permutation for arbitrary List<T> as long as T is Comparable 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@144 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 20:40:26 +00:00
aaron 09d605bb37 Changed how the example walker gets run, I'm about to check in the GNU style command line args. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@143 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 20:10:17 +00:00
depristo 02556ce4a6 Moved to core 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@142 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 20:02:19 +00:00
depristo 1df23b0417 Added a definitely inappropriately placed testing of the new fasta seeking system at the bottom of the file -- it's not called but it probably should be moved to somewhere more appropriate. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@141 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:57:52 +00:00
depristo 611ab0bdb3 Uses the new FastaSequenceFile2 for high-performance seeks. 
Added far superior error checking (and reporting!) messages for incorrect usage of the location string.  Prevents users from seeing complex FunctionalJ error message

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@140 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:56:54 +00:00
depristo e77d735e08 New reference iterator that works with the new FastaSequenceFile seek operations. Greatly improves performance of jumping around in the genome. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@139 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:54:02 +00:00
depristo c8d7207a8e Fixed problem with GenomeLoc logic -- optimization was causing assertion failure. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@138 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:53:00 +00:00
depristo 52ad08298a New FastaSequenceFile with support for poor-man's seek and querying the next contig name without loading the whole next contig into memory. Vastly speeds up the performance of jumping to distant parts of the genome with the location operator. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@137 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:43:56 +00:00
depristo 4888df97c7 Added averageDouble function. How can we write a generic average function?! 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@136 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 19:41:30 +00:00
jmaguire cf407168cf keep track of the position you're called on. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@135 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 16:47:49 +00:00
jmaguire 096f0dbc68 don't run off the end of the list of loci. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@134 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 16:47:29 +00:00
jmaguire 4e0cd6ab84 Now works on single samples and computes metrics. 
Here is an example metrics output from a very tiny region:

	Allele Frequency Metrics (LOD >= 5)
	-------------------------------------------------
	Total loci                         : 14704
	Total called with confidence       : 10920 (74.27%)
	Number of Variants                 : 16 (0.15%) (1/682)
    Fraction of variant sites in dbSNP : 100.00%

Missing:
    Microarray(hapmap) concordance, tp/fp.

Optional:
    Histograms of depth of coverage, LOD, observed allele frequency, etc.



Still to implement:
    Propagate command line argument N (number of chromosomes) into walker to enable pooled calling.
    Take allele frequency priors as input.




git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@133 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 15:45:12 +00:00
jmaguire f7ad17016d some reformatting and logic cleanup in the comparison functions 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@132 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 15:36:56 +00:00
jmaguire dfe50ce773 optionally check that the records are sorted. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@131 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 15:36:24 +00:00
jmaguire 149ac3d96c Now iterate over a large set of tiny intervals efficiently. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@130 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-22 12:04:11 +00:00
asivache df2a7039cb Henious bug fixed: only rookies forget that external conditions need to be re-checked after loop ends on some other condition, duh! In addition, msa piles are now seeded with a single read sequence each (if there are less then 4 reads it might be hard to seed with two pairs) 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@129 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-21 18:32:18 +00:00
kiran 411e5cf647 Added FourBaseCaller as a jar build target. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@128 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-21 17:59:13 +00:00
kiran 6e1fa7d61a Java version of basecaller that estimates probability distribution over four-base hypothesis space via an internal-control-initialized Gaussian mixture model over base channel intensities. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@127 348d0f76-0448-11de-a6fe-93d51630548a
 2009-03-21 17:58:50 +00:00