Releases: broadinstitute/picard
Releases · broadinstitute/picard
2.21.3
2.21.2
- Fix bug in VcfToAdpc Some poor performing sites in VCFs have null normalized X or Y intensity. This fixes the code to handle these.
- Speeds up MarkDuplicates on queryname input by using the in memory read-ends map. (#1411)
- Document two CLPs
- Update plugin versions for github-pages documentation (#1405)
- Removing a spurious newline from the logging output of ReorderSam (#1403)
2.21.1
- Fixing up tests in MarkDuplicates so that tests with duplex UMIs are handled properly. (#1404)
- Make crosscheck take a file->sample map input so that we can crosscheck to a un-duplicated vcf. (#1303)
- Improvements to the locus iteration. (#1376)
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- Added in a progress meter to CollectSamErrorMetrics.
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- Added a flag to enable jumping to loci rather than iterating through all variants / loci in order each run.
- Added a test to CollectHsMetrics to harden against future code changes (#1386)
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- Added a test to CollectHsMetrics to harden against future code changes.
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- removed non-working (and unneeded) code in reflectiveCopy
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- added some protection against NPE
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- cleaned-up some code formatting issues.
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- sanitized some sam files.
2.20.8
- Throw exception in MergeBamAlignments if UNMAPPED_BAM has mapped reads (#1394)
- Order the MarkDuplicatesMetric file (#1398)
- Remove unnecessary import of com.sun.xml.internal class (#1401)
- Propagate errors from threads and add error logging (#1393)
- Fixes a bug in the determination of the distance to the second nearest barcode. (#1395)
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- typo (#1392)
- Revert UpdateVcfSequenceDictionary handles stdout logic and repair test
2.20.7
- Initial Move Calculate the detail metric correctly (on a per-genotype basis). Add more tests Add test to handle multi-sample VCF Refactor detail->summary metrics accumulation. Fix CreateVerifyIDIntensityContaminationMetricsFile to handle LLK and LLK0 as doubles. Added new metric, refined naming of others. Enhanced multiple sample tests.
- Updating gradle to 5.6 (#1380)
- Updating NIO dependency and fixing a dependency issue (#1391)
- Update to htsjdk 2.20.3 (#1381)
- Extend travis build matrix to separate Barclay tests from legacy tests. (#952)
- PO-18867 Catch NaN Percent_Duplication edge case (#1389)
2.20.6
- adding logging to help debug a JVM core-dump (#1387)
- Update instructions for running single tests (#1382)
- ReorderSam was having trouble when new dictionary is larger than old one (#1074)
- relaxing requirements for VCFIndex in tools that don't need one (#1295)
- Add levenshtein distance to eibc (#1331)
- Added a MIN_HISTOGRAM_WIDTH to CollectInsertSizeMetrics. (#1368)
- Adds a buffer to the index stream (#1348)
- revert base image change due to issues building on dockerhub (#1371)
- Upgrades to CompareSAMs (for functional equivalence) (#1305)
2.20.5
- trigger travis with a small commit.
- CreateVerifyIDIntensityContaminationMetricsFile A little program to create a standard picard metrics file from the output of VerifyIDIntensity.
- updating htsjdk to 2.20.0 (#1367)
- Remove docker_helper usage in docker script Remove docker-helper.sh itself Switch base base image to google managed image
- Yf debug sam collector error (#1362)
2.20.4
- GL-422 Move MergePedIntoVCF into picard (#1356)
- MergeSamFiles from cloud (#1346)
- Change default to not throw exception for a call on a zeroed out assay Reverted InfiniumDataFile byteArray <-> Int/Float back to bitwise operations for performance reasons (using ByteBuffer was very slow) Added tests
- Fixes several small issues that needed some help (#1316)
- refactored IntervalListTools to use a "map-reduce" paradigm (#1319)
- Add MIN_TARGET_COVERAGE to HsMetrics (#1345)
- Fix travis build badge (#1357)
- VcfToAdpc a tool to generate an adpc.bin file (Illumina genotyping intensity data) from a Genotyping Arrays VCF.
2.20.3
- Bugfix: Update default platform for IlluminaBasecallsToSam (#1351)
- Recover from side effects introduced in CollectIndependentReplicatesMetric tests. (#1341)
- Adding in some enum constants that are used in existing/old extended manifest files. (#1347)
- Yf provide arbtrary inputs to cmm (#1337)
- GtcToVcf a tool to convert Illumina GTC files to VCF format Responded to a lot (but not all) comments dont recompute tan Refactored some math Enable support for zeroed-out SNPs Generalize AA/AB/BB related fields in VCF Headers Reove zcall from GtcToVcf Added test for GtcToVcf.getGenotypes Use BidiMap Error out / inform user if reference is not HG19 Use IlluminaStrand for Illumina-strand specific fields. Update test to cover all chromosomes used.
- Added whitepaper describing fingerprinting Math (#1247)
- Fixes bug that prevented liftover of spanning deletions. (#1339)
- Removed boilerplate "main" function from picard CLPs. (#1311)
- Trim descriptions to shorten --list display width. (#1259)
- Handle edge cases with no evidence in CrosscheckFingerprints consistently (#1323)