Skip to content

Releases: broadinstitute/picard

3.1.1

14 Nov 22:01
3.1.1
7c65e3c
Compare
Choose a tag to compare

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
Compare
Choose a tag to compare

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
Compare
Choose a tag to compare

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
Compare
Choose a tag to compare

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
Compare
Choose a tag to compare
  • Picard modifications to support flow based sequencing (#1813)

2.27.3

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

2.27.2

25 May 20:09
923403d
Compare
Choose a tag to compare
  • 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
9eafe4e
Compare
Choose a tag to compare
  • Add a new interval list scatter mode (#1786)

2.27.0

06 Apr 21:22
b1e01c2
Compare
Choose a tag to compare
  • Upgrade google-cloud-nio to match gatk (#1792)
  • Add support for documentation generation for metrics classes. (#1782)
  • Simplify handling of paths for input in BuildBamIndex.java (#1787)

2.26.11

23 Feb 22:22
a03ed41
Compare
Choose a tag to compare
  • In GtcToVcf, set infinite values to missing ('.') in the VCF. (#1777)
  • Correct logic to have ExtractBarcodesProgram properly match for all Ns (#1775)
  • Cluster Visualization Python Script (#1701)
  • Detect worker thread exception sooner, and stop other workers. (#1772)