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Releases: broadinstitute/picard

3.3.0

09 Oct 21:03
3.3.0
63138fc
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What's Changed

Argument changes for FLOW based MarkDuplicates

The arguments in MarkDuplicates ) which are specific to flow based reads have been renamed. (by @dror27 #1974)
They're now prefixed with FLOW_ to make it clear when they are relevant. This requires flow read users to update their scripts.

Old New
USE_END_IN_UNPAIRED_READ FLOW_USE_END_IN_UNPAIRED_READS
USE_UNPAIRED_CLIPPED_END FLOW_USE_UNPAIRED_CLIPPED_END.
UNPAIRED_START_UNCERTAINTY FLOW_UNPAIRED_START_UNCERTAINTY
UNPAIRED_END_UNCERTAINTY FLOW_UNPAIRED_END_UNCERTAINTY

New Feature:

RevertSam is now cloud enabled (by @takutosato in #1949)

Bug Fixes

Maintenance

Full Changelog: 3.2.0...3.3.0

3.2.0

27 Jun 13:35
3.2.0
8aa8d6f
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What's Changed

Important CRAM writing bug fix

A serious bug which can cause corrupted reads in CRAM files was discovered and fixed in this release. This bug was introduced in HTSJDK 3.0.0, and affects Picard versions 2.27.3 through 3.1.1 and GATK versions 4.3 through 4.5.

The bug occurs in cases where there is a read aligned starting at exactly position 1 on a reference contig. This means that the bug doesn't generally impact human autosome and X/Y contigs because they tend to start with a large number of N bases and reads are not aligned at exactly position 1. The exceptions to this would be T2T references and things like mitochondrial calling.

For more information on the conditions that trigger this bug, see this post.

GATK 4.6 includes a tool called CRAMIssue8768Detector that can scan a CRAM file and report whether it is affected, and if so which regions in the file are corrupt. If you suspect that some of your CRAM files may have been affected, please run this tool on them for confirmation!

See also samtools/htsjdk#1708 for more information.

Better support for remote files

Improvements to allow direct access to remote files continue. It's now possible to use a remote reference file without localizing it in many cases. Files which are available through http URLs are now accessible directly as well. (ex: https://example.com/my.bam). This allows direct access to signed URLs, although index and supporting files may not be discoverable automatically.

New features for flow based reads

  • MarkDuplicates strategy of flow based reads that looks only at the qualities close to the end of the read by @ilyasoifer in #1942
  • CollectQualityYieldMetricsFlowSpace tool by @dror27 in #1932

New Options

  • KEEP_ZERO_LENGTH_INTERVALS flag when converting bed -> interval_list by @rickymagner in #1928
  • Make the VCF option in CollectSamErrorMetrics optional. by @nh13 in #1476
  • Add the EXT argument to CollectSamErrorMetrics. by @nh13 in #1478

Bug fixes

Bug fixes to several tools as well as important CRAM fixes from an updated htsjdk

  • MarkDuplicates: Add read group ID instead of string "RG" by @michaelgatzen in #1937
  • Fix CollectHSMetrics - Don't use Coverage Cap on fold score by @JoeVieira in #1913
  • Fix for order flipping in SortingCollection used for MarkDuplicates by @wook-choi in #1945
  • Allow fingerprinting of SAM files that only have a partial dictionary match to the haplotype map by @yfarjoun in #1955
  • Fix a bug in the liftover logic by @yfarjoun in #1956

Documentation and improved error messages

  • Reject piped input (/dev/stdin) for BedToIntervalList by @kockan in #1918
  • Update AbstractAlignmentMerger.java Warning Message for Cross Species Contamination by @gokalpcelik in #1960
  • MergeBamAlignment documentation by @kachulis in #1922
  • Updated SamToFastq documentation by @kockan in #1920

Maintenance and dependency updates

New Contributors

Full Changelog: 3.1.1...3.2.0

3.1.1

14 Nov 22:01
3.1.1
7c65e3c
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This is a minor release with a bug fixes and a dependency update.

What's Changed

New Contributors

Full Changelog: 3.1.0...3.1.1

3.1.0

28 Jul 16:45
3.1.0
9470afb
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Cloudy Edition

Highlights

Improving Google Cloud Support

We've done away with the picard-cloud.jar. The default picard jar now includes the necessary libraries to read from google cloud buckets. This is part of an ongoing push to cloud enable more of the important picard tools. It will reduce confusion and simplify code.

  • cloud jar is now default jar #1900
  • IntervalListTools is cloud enabled #1852
  • updated google nio library which supports _ in bucket names #1903
  • new test infrastructure for writing tests that use google cloud #1860

IntelGKL update

A new version

Dependency and Gradle Updates

  • Updated dependencies to their latest versions to incorporate security and bug fixes.
  • Updated to gradle 8.2.1

Notes

  • Downstream toolkits will have to make some changes if they want to continue to NOT provide the google cloud libraries.
  • Updating to gradle 8.2.1 was necessitated by a packaging issue. One of the updated dependencies now includes java 19 code in it's multi-version jar and we needed to update to the newest version of the shadowJar plugin in order to handle it. See #1903 for more disussin.

Change List

New Contributors

Full Changelog: 3.0.0...3.1.0

3.0.0

22 Feb 18:00
3.0.0
04e9b20
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Picard 3.0.0:

The same as before but now on Java 17

The big change is that Picard is moving from Java 8 -> 17.
Java 8 is very old and no longer available by default on most systems. Java 17 is the newest long term support release. This will enable us to take advantage of improvements in the language as well as benefiting from improvements and security fixes in the newer JVMs.

Major changes

Bug fixes and minor improvements

  • Improvements to CompareMetrics by @kachulis in #1839
  • Fix typo in a filter name output by LiftoverVcf by @lbergelson in #1842
  • Stop removing periods from the end of output names by @tlangs in #1433
  • Avoid merging fingerprints when there is only one by @yfarjoun in #1826
  • Remove commons.lang dependency because it is redundant with commons lang3 by @lbergelson in #1856
  • Delete the now redundant ClassFinder by @lbergelson in #1857
  • Remove obsolete references to Google Genomics API by @lbergelson in #1858
  • Fix Duplicate Set Index for queryname sorted input to MarkDuplicates by @kachulis in #1843
  • Allow empty input files for CollectAlignmentSummaryMetrics and FastqToSam by @kachulis in #1859

Documentation and infrastructure changes

Full Changelog: 2.27.5...3.0.0

2.27.5

06 Oct 22:36
2.27.5
533e880
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What's Changed

  • Allow explicit index file paths for inputs to CrosscheckFingerprints by @rickymagner in #1823
  • Fix temporary directory hijacking or temporary directory information disclosure by @lbergelson in #1829
  • Update htsjdk to 3.0.1 by @lbergelson in #1831

Full Changelog: 2.27.4...2.27.5

2.27.4

29 Jun 17:47
c97fce5
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  • Picard modifications to support flow based sequencing (#1813)

2.27.3

09 Jun 20:38
09183c8
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  • Upgrade to htsjdk 3.0.0. (#1812)
  • Fix FastqToSam regression. (#1811)

2.27.2

25 May 20:09
923403d
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  • Update command line parser argument style detection, add tests. (#1785)
  • Convert FastqToSam and RevertSam to use PicardHtsPath (#1794)

2.27.1

07 Apr 17:17
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  • Add a new interval list scatter mode (#1786)