Comparing 3.3.0...3.4.0 · broadinstitute/picard (original) (raw)

Commits on Dec 10, 2024

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Commits on Dec 17, 2024

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Commits on Jan 13, 2025

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Commits on Feb 5, 2025

  1. Fix failures to allocate arrays with a very large Java heap size (#1986)
    The maximum length of a Java array is not exactly Integer.MAX_VALUE,
    but slightly less due to the space taken up by the object header.
    The exact maximum differs depending on the platform and Java
    version. This was already accounted for in one instance, but not
    others. This commit fixes the other instances and changes the
    maximum size in the existing instance to Integer.MAX_VALUE - 32
    instead of Integer.MAX_VALUE - 5 to decrease the likelihood of
    allocation failures on different Java versions and platforms.
    @EthanNelson-Moore
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Commits on Feb 11, 2025

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Commits on Mar 11, 2025

  1. fix: documentation errors. (#1998)
    closes: #1996
    The documentation in HsMetrics class was inaccurate regarding the filtering of reads that go into the PCT_USABLE_BASES_ON_BAIT. It now correctly reflects the fact that the reads/bases that go into this calculation are not unique, i.e. duplicate reads are counted.
    @yfarjoun
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Commits on Mar 19, 2025

  1. Optionally extract all fingerprint snps (#1989)
    Currently ExtractFingerprints only writes out the representative SNP for each haplotype block. While this is useful for the intended use-case (of creating a fingerprint and then using it subsequently in crosscheck or some such) there are other use-cases where it can be useful to know the genotype/PL at all the fingerprinting SNPs in each block.
    Added a new argument EXTRACT_NON_REPRESENTATIVES_TOO to output all SNPs in each block.
    @yfarjoun
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Commits on Apr 13, 2025

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