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                                            Jay Carey

Proposal to change maintainers

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Added validation warning if the mapped length of the read is greater than the predicted insert size for FR pairs on the same chromosome.

CramFileReader constructor with file, stream and refsource doesn't set a validation stringency and so it was null which caused processValidationErrors in SamUtils to ignore the error since previously it was...

Added validation warning if the mapped length of the read is greater than the predicted insert size for FR pairs on the same chromosome.

Also as a note I'm a fair amount of these warning spit out on test run. We have a lot of test data that fails this check (usually adapter clipped...

GroupReadsByUmi Error java.nio.file.NoSuchFileException: /dev/stdin

Hi @Emmalynchen. Can you let me know what shell you are using? There is a check that we do when creating an inputstream to determine if the path you are...