Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Spotbugs remaining fixes #1331

Merged
merged 14 commits into from
Mar 18, 2019
Merged

Spotbugs remaining fixes #1331

merged 14 commits into from
Mar 18, 2019

Commits on Mar 18, 2019

  1. SpotBugs

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    0390acc View commit details
    Browse the repository at this point in the history

  2. Ignore clone/Cloneable warning

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    fc3dec4 View commit details
    Browse the repository at this point in the history

  3. MergingSamRecordIterator and SortingCollection are not actually Seria… 

    …lizable.
    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    f6309fc View commit details
    Browse the repository at this point in the history

  4. Remove unnecessary check (it's known that i3 > -1 at this point)

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    452bdf5 View commit details
    Browse the repository at this point in the history

  5. Deprecate IOUtils#VCF_EXTENSIONS since it is a public mutable array.

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    212414e View commit details
    Browse the repository at this point in the history

  6. Ignore gc warning

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    a8656bd View commit details
    Browse the repository at this point in the history

  7. Ignore Thread.start() warning in constructor of AbstractAsyncWriter

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    3ab170b View commit details
    Browse the repository at this point in the history

  8. Ignore redundant null check in htsjdk.variant.vcf.AbstractVCFCodec

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    c672089 View commit details
    Browse the repository at this point in the history

  9. Clarify that inherited (not outer) method hasNext() is being called b… 

    …y TupleIterator
    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    6482343 View commit details
    Browse the repository at this point in the history

  10. Ignore warning in HTTPHelper about writing to a static field from an … 

    …instance.
    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    a5abccd View commit details
    Browse the repository at this point in the history

  11. Ignore test for floating point equality in Histogram and LinearIndex

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    09cd583 View commit details
    Browse the repository at this point in the history

  12. Fix NPE

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    2e7f566 View commit details
    Browse the repository at this point in the history

  13. Preserve existing behaviour of TextualBAMIndexWriter

    @tomwhite @lbergelson
    tomwhite authored and lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    a2ef207 View commit details
    Browse the repository at this point in the history

  14. run spotBugs on travis

    @lbergelson
    lbergelson committed Mar 18, 2019
    Configuration menu
    Copy the full SHA
    07510fc View commit details
    Browse the repository at this point in the history