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Error with the bedtools merge function

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N Cerda

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Jun 14, 2021, 7:22:31 PM6/14/21
to bedtools-discuss
Hi I believe the merge function may not be functioning properly.
I'm executing the following command: 
bedtools merge -s -c 6 -o distinct -d 200 -i Athaliana_hmm_e00005.bed

My input data:
1 11896548 11896704 . . -
1 11896785 11897244 . . -
1 12678495 12679080 . . +
1 12723287 12723953 . . -
1 12833400 12834042 . . -
1 13187287 13188100 . . -
1 13269707 13270250 . . -
1 13611137 13611404 . . -
1 14049097 14049739 . . +
1 14226222 14226468 . . -
1 14226532 14226739 . . -

And I get the following output:
1       11896785        11897244        -
1       12678495        12679080        +
1       12723287        12723953        -
1       12833400        12834042        -
1       13187287        13188100        -
1       13269707        13270250        -
1       13611137        13611404        -
1       14049097        14049739        +
1       14226532        14226739        -

I have signaled in bold the problematic lines. As it can be seen in the output, instead of merging the lines, and keeping the lowest start position and the highest end of close ranges, the program only deletes a line and doesn't change the values.

I hope you can help me see if I'm making a mistake when using the program or if this is actually a bug and can be fixed. Thank you!

Navei.

Aaron Quinlan

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Jun 15, 2021, 6:15:52 PM6/15/21
to bedtools...@googlegroups.com
Dear Navei,

I am unable to reproduce this problem with version 2.30.0. I receive the expected output.
Could you kindly try this latest version to test whether it resolves your issue?

Thanks,
Aaron

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