Hi,

I have noticed for a while now that BED files are not recognized correctly or at least not parsed out correctly.

I notice that invariably, the (9 column) BED file comments state there is 1 region and X comments, where X + 1 is the actual number of regions in the file..

Here's a few lines from the file

1	38076950	38077349	utr3:RSPO1	1	-	38077349	38077349	0,0,255
1	38077420	38078426	utr3:RSPO1	1	-	38078426	38078426	0,0,255
1	38078426	38078593	cds:RSPO1	1	-	38078426	38078593	255,0,0
1	38079375	38079564	cds:RSPO1	1	-	38079375	38079564	255,0,0
1	38079855	38080005	cds:RSPO1	1	-	38079855	38080005	255,0,0
1	38082155	38082347	cds:RSPO1	1	-	38082155	38082347	255,0,0
1	38095239	38095333	cds:RSPO1	1	-	38095239	38095333	255,0,0
1	38095333	38095621	utr5:RSPO1	1	-	38095621	38095621	0,0,255

Any ideas why it thinks there are comments in the file and why only one region?

The file is a regular txt file without the LF and is not DOS format or anything...

It also does not parse out the name, score and strand info, but once I correct that manually, it works, but it is a pain to have to do that everytime...

Thanks,

Thon

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