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Changed SAMRecord.toString() to emit the SAM format string with all fields#1762

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tfenne wants to merge 1 commit intomasterfrom
tf_getter_samrecord_tostring
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Changed SAMRecord.toString() to emit the SAM format string with all fields#1762
tfenne wants to merge 1 commit intomasterfrom
tf_getter_samrecord_tostring

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@tfenne tfenne commented Mar 30, 2026

Description

SAMRecord has historically output an abbreviated format in toString(). I think more often than not this is confusing to users, since a SAMRecord has a well defined String format. Moreover the toString() method is used extensively by TestNG to display when two SAMRecord instances are not equal - and the vast majority of the time the toString() output did not contain the differences.

Things to think about before submitting:

  • Make sure your changes compile and new tests pass locally.
  • Add new tests or update existing ones:
    • A bug fix should include a test that previously would have failed and passes now.
    • New features should come with new tests that exercise and validate the new functionality.
  • Extended the README / documentation, if necessary
  • Check your code style.
  • Write a clear commit title and message
    • The commit message should describe what changed and is targeted at htsjdk developers
    • Breaking changes should be mentioned in the commit message.

@tfenne tfenne requested a review from yfarjoun March 30, 2026 19:59
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