sorting and merging interval lists, and creating RODs from intervals. This
gives Doug the ability to keep using our interval list parsing code when
sorting intervals on our behalf.
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Using this feature, sites covered by the target ROD will be iterated over. This list of intevals generated is merged with any intervals from the -L and -XL args, and the Walker is run over the resulting merged list.
WARNING: for very large ROD's this can be costly. Consider this experimental for now.
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Most of the changes occur in GenomeAnalysisEngine.java and GenomeLocParser.java:
-- parseIntervalRegion and parseGenomeLocs combined into parseIntervalArguments
-- initializeIntervals modified
-- some helper functions deprecated for cleanliness
Includes new set of unit tests, GenomeAnalysisEngineTest.java
New restrictions:
-- all interval arguments are now checked to be on the reference contig
-- all interval files must have one of the following extensions: .picard, .bed, .list, .intervals, .interval_list
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a caveat: for anyone asking for all of the ROD's back from the RefMetaDataTracker (if your not using the facilities to get the track by name), you'll now be getting back a collection of GATKFeature objects. This object will contain the track name, and a method for getting the underlying object (getUnderlyingObject()), which will be the traditional RodVCF, rodDbSNP, etc. This layer is needed so we can integrate Tribble tracks (which don't natively have names). Calls that ask for RODs by name will still get back the traditional reference ordered data objects (RodVCF, rodDbSNP, etc).
Sorry for the inconvenience! More changes to come, but this is by far the largest (as has the greatest effect on end users).
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Introducing this into the pile of code which peeks under the covers of the SAMDataSource in the hopes
that this function can help to replace the others and provide a single path for crosstalk.
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merging lots of BAMs, and the fix is taking longer than I thought. Disable
experimental sharding when merging until the fix is ready.
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+ -L all now walks over all intervals
+ if a -L argument is passed with a .list extension, and file does not exist, returns a \
File Not Found error instead of "bad interval" error. We plan to soon revisit interval \
lists and generate a concrete list of filenames, so this is likely temporary.
+ Error is thrown if the start position on an interval is higher number than the end position.
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infrastructure can be torn down:
1) New sharding system emulates old MonolithicSharding mechanism.
2) Better awareness of differences between fasta and BAM files when creating
shards.
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GATK users from the readers, which they could abuse in ways that could destabilize the GATK.
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simplification of some of the locus traversal code.
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Now the IndelRealigner can use this functionality without being forced to merge abutting intervals (which was actually causing a problem with the cleaning).
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In indel cleaner:
1. allow the user to specify that he wants to use Picardâs SAMFileWriter sorting on disk instead of having us sort in memory; this is useful if the input consists of long reads.
2. for N-way-out mode: output bams now use the original headers from the corresponding input bams - as opposed to the merged header. This entailed some reworking of the datasources code.
3. intermediate check-in of code that allows user to input known indels to be used as alternate consenses. Not done yet.
In UG: fix bug in beagle output for Jared.
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2. Used said mapping to implement N-way-in,N-way-out functionality in the new indel cleaner. Still needs more testing (to be done after vacation but preliminary tests look good).
3. Fixes to VCF validator: ignore case when testing VCF reference base against true reference base and allow quals of -1 (as per spec).
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support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
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* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
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1: all overlapping and abutting intervals merged (ALL),
2: just overlapping, not abutting intervals (OVERLAPPING_ONLY),
3: no merging (NONE). This option is not currently allowed, it will throw an exception. Once we're more certain that unmerged lists are going to work in all cases in the GATK, we'll enable that.
The command line option is --interval_merging or -im
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shard for cases when the index file isn't available. Works for the case in question, but is not
guaranteed to work in general. Will be replaced once the new sharding system comes online.
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and displays walker data extracted from the JavaDoc. Needs a bit of help,
both in content and flexibility of package naming.
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Just stomped on the existing md5s because that's what Eric told me to do.
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Revert until we find out whether the cause is legit.
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hanna
aaron
bthomas
ebanks
kshakir
depristo
asivache
rpoplin