There's a problem that has been an issue for a long time, and that is duplicates in the added feature columns. The same feature can get added as annotation to a data row multiple times. Here's an example:
Output:
>cat JS11_bamCoverage.bedgraph.nocov.simple
#featureProximity.pl Version 3.8
# Created: 11/2/2011
# Last modified: Wed Mar 15 16:13:59 2017
#Wed Mar 15 16:14:46 2017
#/usr/bin/perl /Users/rleach/pub/seqtools/featureProximity.pl -i deletions_unique.txt -f JS11_bamCoverage.bedgraph.nocov -r 0 -c 1 -b 2 -e 3 -a 1 -j 2 -k 3 -w 1
#datcol(1) datcol(2) datcol(3) Distance ftcol(1)
1 33574 33575
1 36126 36141
1 580578 580581
1 2078797 2078798 0 1,1
1 2622551 2622908
1 2652306 2652316 0 1
1 2653569 2653597
1 2653683 2653691 0 1,1
1 2743286 2743305 0 1,1
1 2744893 2744896
1 2745174 2745199 0 1
1 2850668 2850689
1 2852896 2852903 0 1
1 3062741 3062792 0 1
1 3071674 3071683 0 1
1 3127342 3127343
1 3178221 3178235 0 1,1
1 3217467 3217492 0 1,1
1 3223021 3223022
2 26955 26956
2 136633 136669 0 2
2 1021481 1021482
2 1021487 1021488 0 2,2
2 1022198 1022199
2 1334133 1334134 0 2,2
2 1776702 1777433
Note the "1,1" and "2,2" feature annotations. Those are duplicate matches separated by commas. There is really only 1 such feature that overlaps the matching positions. Note the inputs below:
Inputs:
>cat JS11_bamCoverage.bedgraph.nocov
1 37318 37335 0
1 1895314 1895318 0
1 2078797 2078798 0
1 2410087 2410091 0
1 2652314 2652315 0
1 2653071 2653169 0
1 2653683 2653690 0
1 2743286 2743301 0
1 2745176 2745197 0
1 2851251 2851256 0
1 2852897 2852901 0
1 3060846 3060899 0
1 3061005 3061065 0
1 3061165 3061179 0
1 3062772 3062781 0
1 3066730 3066852 0
1 3071681 3071682 0
1 3072186 3072347 0
1 3110774 3110988 0
1 3112783 3112785 0
1 3117996 3118031 0
1 3121421 3121471 0
1 3178226 3178235 0
1 3178327 3178337 0
1 3217490 3217492 0
2 134711 134715 0
2 135204 135328 0
2 136639 136661 0
2 1021487 1021488 0
2 1334133 1334134 0
>cat deletions_unique.txt
1 33574 33575
1 36126 36141
1 580578 580581
1 2078797 2078798
1 2622551 2622908
1 2652306 2652316
1 2653569 2653597
1 2653683 2653691
1 2743286 2743305
1 2744893 2744896
1 2745174 2745199
1 2850668 2850689
1 2852896 2852903
1 3062741 3062792
1 3071674 3071683
1 3127342 3127343
1 3178221 3178235
1 3217467 3217492
1 3223021 3223022
2 26955 26956
2 136633 136669
2 1021481 1021482
2 1021487 1021488
2 1022198 1022199
2 1334133 1334134
2 1776702 1777433
I suspect that this issue has to do with separate loops that search for features with different orientations or searches different ways relative to the data coordinates. I recall having looked into this in the past and I remember that it was a difficult bug to resolve.
There's a problem that has been an issue for a long time, and that is duplicates in the added feature columns. The same feature can get added as annotation to a data row multiple times. Here's an example:
Output:
Note the "1,1" and "2,2" feature annotations. Those are duplicate matches separated by commas. There is really only 1 such feature that overlaps the matching positions. Note the inputs below:
Inputs:
I suspect that this issue has to do with separate loops that search for features with different orientations or searches different ways relative to the data coordinates. I recall having looked into this in the past and I remember that it was a difficult bug to resolve.