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  • coverageBed -split giving incorrect output?

    In the command below, coverageBed seems to be ignoring the -split argument.

    $ coverageBed -split -a a2.bed -b b2.bed > out.txt

    (The inputs and the output for the command above are shown below in addition to being attached.)

    Please note that b2.bed defines two blocks, each of width 1960, and that a2.bed defines a single block of length 50 that is between those two blocks and does not intersect them. Yet, in out.txt the 13th field has a 1 in it, indicating that there was an overlap. Also, the 15th field in out.txt is the distance from the beginning of the first block of b2.bed to the end of the last block of b2.bed. I think it should be 1960+1960.

    What am I doing wrong? Any help appreciated.
    I'm running v2.12.0 of coverageBed.
    Thanks. -Ben

    $ cat a2.bed
    chrX 5561936 5561986 56_1638_1187_F3 50 - 5561936 5561986 255,0,01 50 0

    $ cat b2.bed
    chrX 4074963 30247441 eg:668963:chrX 0 + 4074963 4076923 0 2 1960,1960, 0,26170518,

    $ cat out.txt
    chrX 4074963 30247441 eg:668963:chrX 0 + 4074963 4076923 0 2 1960,1960, 0,26170518, 1 50 26172478 0.0000019
    Attached Files

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