BR: gappedPeak contains invalid block coordinates

[balwierz]

My gappedPeak output contains overlapping blocks.

contig1      0       350     Peak_205958     1000    .       0       340     255,0,0 3       1,340,1 0,0,349 2233.0  -1      -1
contig2      12830   14320   Peak_205966     1000    .       12850   14320   255,0,0 3       1,1470,1        0,20,1489       57.0    -1      -1
contig3      10970   12440   Peak_350732     1000    .       12090   12440   255,0,0 3       1,350,1 0,1120,1469     45.0    -1      -1

In the first line blocks 0 and 1 overlap (they both start at 0) In the second line blocks 1 and 2 overlap (1470+20 > 1489) In the third case blocks 1 and 2 overlap (1120+350 > 1469)

There are more cases like this. They appear at first or last peaks at a given chromosome contig. Seems to me like some off-by-one kind of issue.

Expected behavior gappedPeak containing non-overlapping blocks.

System (please complete the following information):

• OS: Debian testing
• openjdk 11.0.8
• HMMRATAC 1.2.10

[EvanTarbell]

Thanks for the report! I'll look into fixing that ASAP.