Chris, if this breaks an integration test, you get it.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1879 348d0f76-0448-11de-a6fe-93d51630548a
also: their, I hope your happy Eric, from now on I'll try not to flout my awesomest grammer in the future accept when I need to illicit a strong response :-)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1858 348d0f76-0448-11de-a6fe-93d51630548a
Remove all sequenom stuff from the FastaAlternateReferenceMaker so it can just concentrate on making alternate references...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1831 348d0f76-0448-11de-a6fe-93d51630548a
Also a fix to the GLF tests, and a correction to PrintReadsWalker to remove the close() on the output source, the source handles that itself (and you get a double close).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1758 348d0f76-0448-11de-a6fe-93d51630548a
PARTIAL commit; new, simpler rodRefSeq will reappear in a seq.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1694 348d0f76-0448-11de-a6fe-93d51630548a
all the updated classes now make use of new SeekableRodIterator instead of RODIterator. RODIterator class deleted. This batch makes only trivial updates to tests dictated by the change in the ROD system interface. Few less trivial updates to follow. This is a partial commit; a few walkers also still need to be updated, hold on...
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1667 348d0f76-0448-11de-a6fe-93d51630548a
The main reason for the change is that there can be (and are!) multiple RODs overlapping with a single reference base position in a single track. There can be two "trivial" RODs at the same location (e.g. samtools pileup will have two point-like records at putative indel sites: one for the reference, the other one for the indel itself). Or there can be one or more "extended" RODs (length >1), eg. dbSNP can report an indel at Z:510-525 AND a SNP at Z:515.
The ReferenceOrderedDatum object (and children) will not be changed, but it is now explicitly interpreted as a single data *record*, possibly out of many available from a given track for the current site. As long as single data record occupies one line in a data file, the new ROD system will take care of loading and keeping multiple records, including extended (length > 1) ones, and will automatically drop the records when they finally go out of scope. For one-line-per-record, multiple-records-per-site RODs, there is no need anymore for the hack used so far that involved passing ROD's own implementation of iterator through reflection mechanism (though it will still work)
* RODRecordList:
the ROD system (its iterators) will now always return a LIST of all RODs available at current position or at current query interval (see below). This class is a trivial wrapper for a list of ROD objects, with added location argument for the whole collection. The location of the RODRecordList is where the ROD system is currently sitting at: a single, current base on the reference (if next() traversal is performed), or the location of the query interval when returned by seekForward() (see below). The ROD objects themselves will have their locations set according to the original data in the file. Hence, perusing the above example of a dbSNP indel at Z:510-525 and SNP at Z:515, when moving to the position Z:515 the ROD system will return a RODRecorList with location Z:515, and with two ROD objects packaged inside, one with location Z:510-525, the other with Z:515.
*RODRecodIterator:
Almost identical to old SimpleRODIterator used by ReferenceOrderedData; this is a low-level iterator that walks over records in the data file (with a callback to ROD's ::parseLine() to parse real data)
*SeekableRODIterator:
a decorator class that wraps around Iterator<ROD> (such as RODRecordIterator) and makes the data traversable by reference position, rather than record by record. This is reimplementation of the old RODIterator. SeekableRODIterator's ::next() moves to the next position on the ref and returns all RODs overlapping with that position (as a RODRecordList). This iterator also adds a seekForward(loc) operation, that allows fast forwarding to a specified position or interval. Length > 1 query arguments (extended intervals) are fully supported by seekForward(), the returned RODRecordList wil contain all RODs overlapping with the specified interval, and the location of the returned RODRecordList object will be set to that query interval. NOTE: it is ILLEGAL to perform next() after a seekForward() query with length > 1 interval. seekForward() with point-like (length=1) interval reenables next().
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1650 348d0f76-0448-11de-a6fe-93d51630548a
Rollback of Variant-related changes of r1585, additional PGC code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
1) Moved various disparate concordance / set splitting functionalities to a new parent tool which works like VariantFiltration (i.e. people can write various modules that fit inside and can be run though it).
2) Fixed up argument parsing in VariantFiltration to use key=value format so we don't accidentally mox up values (like I had been doing).
3) Have indel rod print samples
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1540 348d0f76-0448-11de-a6fe-93d51630548a
-Remove KGenomesSNPROD
-Remove rodFLT
-Renamed rodGFF to RodGenotypeChipAsGFF
-Fixed a problem in SSGenotypeCall
-Added basic SSGenotype Test class
-Make VCFHeader constructors public
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1536 348d0f76-0448-11de-a6fe-93d51630548a
aaron
asivache
ebanks
depristo
chartl