coverageBed from version 2.15 fails to prduce the correct depth of coverage if split option was selected

[GoogleCodeExporter]

What steps will reproduce the problem?

1. coverageBed -abam test.bam -b test.bed -split -d

What is the expected output? What do you see instead?

Expected output:

chr7    98792644    98792674    1   0
chr7    98792644    98792674    2   0
chr7    98792644    98792674    3   0
chr7    98792644    98792674    4   0
chr7    98792644    98792674    5   0
chr7    98792644    98792674    6   0
chr7    98792644    98792674    7   1
chr7    98792644    98792674    8   1
chr7    98792644    98792674    9   1
chr7    98792644    98792674    10  1
chr7    98792644    98792674    11  1
chr7    98792644    98792674    12  1
chr7    98792644    98792674    13  2
chr7    98792644    98792674    14  2
chr7    98792644    98792674    15  2
chr7    98792644    98792674    16  2
chr7    98792644    98792674    17  2
chr7    98792644    98792674    18  2
chr7    98792644    98792674    19  2
chr7    98792644    98792674    20  3
chr7    98792644    98792674    21  3
chr7    98792644    98792674    22  3
chr7    98792644    98792674    23  3
chr7    98792644    98792674    24  3
chr7    98792644    98792674    25  3
chr7    98792644    98792674    26  3
chr7    98792644    98792674    27  3
chr7    98792644    98792674    28  3
chr7    98792644    98792674    29  3
chr7    98792644    98792674    30  3

I see this instead:

chr7    98792644        98792674        1       0
chr7    98792644        98792674        2       0
chr7    98792644        98792674        3       0
chr7    98792644        98792674        4       0
chr7    98792644        98792674        5       0
chr7    98792644        98792674        6       0
chr7    98792644        98792674        7       0
chr7    98792644        98792674        8       0
chr7    98792644        98792674        9       0
chr7    98792644        98792674        10      0
chr7    98792644        98792674        11      0
chr7    98792644        98792674        12      0
chr7    98792644        98792674        13      0
chr7    98792644        98792674        14      0
chr7    98792644        98792674        15      0
chr7    98792644        98792674        16      0
chr7    98792644        98792674        17      0
chr7    98792644        98792674        18      0
chr7    98792644        98792674        19      0
chr7    98792644        98792674        20      0
chr7    98792644        98792674        21      0
chr7    98792644        98792674        22      0
chr7    98792644        98792674        23      0
chr7    98792644        98792674        24      0
chr7    98792644        98792674        25      0
chr7    98792644        98792674        26      0
chr7    98792644        98792674        27      0
chr7    98792644        98792674        28      0
chr7    98792644        98792674        29      0
chr7    98792644        98792674        30      0

What version of the product are you using? On what operating system?

Version 2.15 on linux.

Please provide any additional information below.

Versions 2.12, 2.14.2 and 2.16 all produce the correct output.

Original issue reported on code.google.com by tiagolc...@gmail.com on 14 Jun 2012 at 1:49

Attachments:

• test.bam
• test.bed

[GoogleCodeExporter]

Please test with the latest version 2.16.2, as several bugs and enhancements 
have been made for -split.

Original comment by aaronqui...@gmail.com on 14 Jun 2012 at 2:05

[GoogleCodeExporter]

Original comment by aaronqui...@gmail.com on 19 Jun 2012 at 4:57

• Changed state: Invalid