GATKReport format changes:
- All non-data header lines are preceeded with a single pound ( #:)
- Every report now has a report header containing the version number and number of tables
- Every table has two lines of table header: The first explains the size of the table and the data types of each column, the second contains the table name and description.
- This new format will allow reports in the future to be gatherable.
- Changed the header format to include an end-of-line string ":;"
Added features:
- Simplified GATK Reports:
The constructor for a simplified GATK Report. Simplified GATK report are designed for reports that do not need the advanced functionality of a full GATK Report.
A simple GATK Report consists of:
- A single table
- No primary key ( it is hidden )
Optional:
- Only untyped columns. As long as the data is an Object, it will be accepted.
- Default column values being empty strings.
Limitations:
- A simple GATK report cannot contain multiple tables.
- It cannot contain typed columns, which prevents arithmetic gathering.
- Added a constructor to generate simplified GATK reports.
- Added a method to easily add data to simple GATK reports.
- Upgraded the input parser take advantage of the new file format (v1).
- Added the GATKReportGatherer, more usability cmoing in next versionof GATK Report. Curently, it can only add rows from one table to another. Added private methods in GATKReport to combine Tables and Reports, It is very conservative and will only gather if the table columns, as well as everything else matches. At the column level, it uses the (redundant) row ids to add new rows. It will throw an exception if it is overwriting data.
- Made some GATKReport methods public, and added more setters and getters.
- Added method that compares formats of two GATKReports, and added an equals method to verify all data inside.
- The gsalib for R now supports reading GATKReport v1 files in addition to legacy formats (v0.*)
- Added a GATKReportDataType enum to give column a certain data type. This must be specified when making a gatherable report. This enum contains several methods including a reverse lookup map.
- Added a data type field in GATKColumn, when a type is not specified, the unknown type is used. Unknown types should not be gathered.
Test changes:
- Updated Unit Tests for GATK Report v1. Added a test for the gatherer. Left one test disabled while we transition from v0 to v1.
- Updated the MD5 hashes in integration tests throughout the GATK.
Other changes:
- Added the gatherer functions to CoverageByRG
- Also added the scatterCount parameter in the Interval Coverage script
- Dropped support for reading in legacy GATKReport formats ( v0.*)
- Updated VariantEvalWalker to work with GATK Report v1, added a format String to all applicable DataPoints.
- Rewrote the read file method for GATK report files.
- Optimized the equals methods within GATKReport. The protected functions should only be called by the GATKReport methods.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Several of the unit tests for the new key authorization feature require
read access to the GATK master private key file. Since this file is only
readable by members of the group gsagit, this makes it hard for people
outside the group to run the test suite.
Now, we skip tests that require the master private key if the private
key exists (since not existing would be a true error) but is not readable
by the user running the test suite
Bamboo, of course, will always be able to run these tests.
-Running the GATK with the -et NO_ET or -et STDOUT options now
requires a key issued by us. Our reasons for doing this, and the
procedure for our users to request keys, are documented here:
http://www.broadinstitute.org/gsa/wiki/index.php/Phone_home
-A GATK user key is an email address plus a cryptographic signature
signed using our private key, all wrapped in a GZIP container.
User keys are validated using the public key we now distribute with
the GATK. Our private key is kept in a secure location.
-Keys are cryptographically secure in that valid keys definitely
came from us and keys cannot be fabricated, however keys are not
"copy-protected" in any way.
-Includes private, standalone utilities to create a new GATK user key
(GenerateGATKUserKey) and to create a new master public/private key
pair (GenerateKeyPair). Usage of these tools will be documented on
the internal wiki shortly.
-Comprehensive unit/integration tests, including tests to ensure the
continued integrity of the GATK master public/private key pair.
-Generation of new user keys and the new unit/integration tests both
require access to the GATK private key, which can only be read by
members of the group "gsagit".
* Turns DNA sequences (for context covariates) into bit sets for maximum compression
* Allows variable context size representation guaranteeing uniqueness.
* Works with long precision, so it is limited to a context size of 31 bases (can be extended with BigNumber precision if necessary).
* Unit Tests added
* added support to base before deletion in the pileup
* refactored covariates to operate on mismatches, insertions and deletions at the same time
* all code is in private so original BQSR is still working as usual in public
* outputs a molten CSV with mismatches, insertions and deletions, time to play!
* barely tested, passes my very simple tests... haven't tested edge cases.
* new unit tests for the alignment shift properties of reduce reads
* moved unit tests from ReadUtils that were actually testing GATKSAMRecord, not any of the ReadUtils to it.
* cleaned up ReadUtilsUnitTest
Eric reported this bug due to the reduced reads failing with an index out of bounds on what we thought was a deletion, but turned out to be a read starting with insertion.
* Refactored PileupElement to distinguish clearly between deletions and read starting with insertion
* Modified ExtendedEventPileup to correctly distinguish elements with deletion when creating new pileups
* Refactored most of the lazyLoadNextAlignment() function of the LocusIteratorByState for clarity and to create clear separation between what is a pileup with a deletion and what's not one. Got rid of many useless if statements.
* Changed the way LocusIteratorByState creates extended event pileups to differentiate between insertions in the beginning of the read and deletions.
* Every deletion now has an offset (start of the event)
* Fixed bug when LocusITeratorByState found a read starting with insertion that happened to be a reduced read.
* Separated the definitions of deletion/insertion (in the beginning of the read) in all UG annotations (and the annotator engine).
* Pileup depth of coverage for a deleted base will now return the average coverage around the deletion.
* Indel ReadPositionRankSum test now uses the deletion true offset from the read, changed all appropriate md5's
* The extra pileup elements now properly read by the Indel mode of the UG made any subsequent call have a different random number and therefore all RankSum tests have slightly different values (in the 10^-3 range). Updated all appropriate md5s after extremely careful inspection -- Thanks Ryan!
phew!
* if the adaptor boundary is more than MAXIMUM_ADAPTOR_SIZE bases away from the read, then let's not clip anything and consider the fragment to be undetermined for this read pair.
* updated md5's accordingly
* Knuth-shuffle is a simple, yet effective array permutator (hope this is good english).
* added a simple randomSubset that returns a random subset without repeats of any given array with the same probability for every permutation.
* added unit tests to both functions
* Modified cleanCigarShift to allow insertions in the beginning and end of the read
* Allowed cigars starting/ending in insertions in the systematic ReadClipper tests
* Updated all ReadClipper unit tests
* ReduceReads does not hard clip leading insertions by default anymore
* SlidingWindow adjusts start location if read starts with insertion
* SlidingWindow creates an empty element with insertions to the right
* Fixed all potential divide by zero with totalCount() (from BaseCounts)
* Updated all Integration tests
* Added new integration test for multiple interval reducing
These functions are methods of the read, and supplement getAlignmentStart() and getUnclippedStart() by calculating the unclipped start counting only soft clips.
* Removed from ReadUtils
* Added to GATKSAMRecord
* Changed name to getSoftStart() and getSoftEnd
* Updated third party code accordingly.
The algorithm wasn't accounting for the case where the read is the reverse strand and the insert size is negative.
* Fixed and rewrote for more clarity (with Ryan, Mark and Eric).
* Restructured the code to handle GATKSAMRecords only
* Cleaned up the other structures and functions around it to minimize clutter and potential for error.
* Added unit tests for all 4 cases of adaptor boundaries.
* New ClippingOp REVERT_SOFTCLIPPED_BASES turns soft clipped bases into matches.
* Added functionality to clipping op to revert all soft clip bases in a read into matches
* Added revertSoftClipBases function to the ReadClipper for public use
* Wrote systematic unit tests
fixed issue where a read starting with an insertion followed by a deletion would break, clipper can now safely clip the insertion and the deletion if that's the case.
note: test is turned off until contract changes to allow hanging insertions (left/right).
* fixed edge case when requested to hard clip beginning of a read that had hanging soft clipped bases on the left tail.
* fixed edge case when requested to hard clip end of a read that had hanging soft clipped bases on the right tail.
* fixed AlignmentStart of a clipped read that results in only hard clips and soft clips
note: added tests to all these beautiful cases...
* expanded the systematic cigar string space test framework Roger wrote to all tests
* moved utility functions into Utils and ReadUtils
* cleaned up unused classes
caught a bug in the hard clipper where it does not account for hard clipping softclipped bases in the resulting cigar string, if there is already a hard clipped base immediately after it.
* updated unit test for hardClipSoftClippedBases with corresponding test-case.
bug: When performing multiple hard clip operations in a read that has indels, if the N+1 hardclip requests to clip inside an indel that has been removed by one of the (1..N) previous hardclips, the hard clipper would go out of bounds.
fix: dynamically adjust the boundaries according to the new hardclipped read length. (this maintains the current contract that hardclipping will never return a read starting or ending in indels).
-- Now properly handles the case where a sample isn't present (no longer adds a null to the genotypes list)
-- Fix for logic failure where if the number of requested samples equals the number of known genotypes then all of the records were returned, which isn't correct when there are missing samples.
-- Unit tests added to handle these cases
Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
*Still needs debugging because code is not working.
Created test classes to be used across several tests.
Some cases are still commented out.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
Insertions are a problem so cigar cases with "I" are commented out.
The test works with multiple deletions and matches.
This is still not a complete test. A lot of cigar test cases are commented out.
Added insertions to ReadClipperUnitTest
ReadClipper now tests for all indels.
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
David Roazen
Roger Zurawicki
Ryan Poplin
Mauricio Carneiro
Mark DePristo
Khalid Shakir
Matt Hanna