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Published 20 hours ago • verified publisher icon mozack

Bed file format

Open V-Catherine opened this issue 5 years ago • 1 comments

My bed file with its one-line header made abra2 crash with the following error: Loading target regions from : target.bed Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 1 at abra.RegionLoader.load(RegionLoader.java:49) at abra.ReAligner.getRegions(ReAligner.java:1347) at abra.ReAligner.loadRegions(ReAligner.java:1379) at abra.ReAligner.reAlign(ReAligner.java:180) at abra.ReAligner.run(ReAligner.java:1833) at abra.Abra.main(Abra.java:12) Once I removed the header line, it run well. Many bed files have headers so maybe it would be useful to allow them. Thanks in advance

V-Catherine avatar Jun 18 '20 12:06 V-Catherine

We currently skip header lines starting with what I understand to be the standard bed header text. i.e. browser, track or #

Let me know if you are seeing otherwise.

mozack avatar Sep 14 '20 17:09 mozack