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JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Allow to change BED format for tracks. #238

Closed iromeo closed 9 months ago

iromeo commented 11 months ago

Sometimes BED file are corrupted or partly follow to BED specification, e.g. this is BED9 in first 2 lines and BED8+1 in 3-rd line

chr1    10435374    10435526    ARNTL:U2OS  1   .   10435434    10435435    168,112,168
chr1    10450320    10450472    ARNTL:U2OS  1   .   10450423    10450424    168,112,168
chr1    10472348    10472744    ARNTL:Hep-G2,GSC,U2OS   4   .   10472559    10472560    168,112,168,207,254,82
chr1    10474844    10475164    ARNTL:Hep-G2,GSC,NSC    3   .   10474985    10474986    168,112,168
chr1    10494189    10494353    ARNTL:U2OS  1   .   10494309    10494310    168,112,168

As a result we get track error, that BED entry can't be parsed with bed9, but auto format for that entry is a bed9. Let's allow user to fix BED format & reload track (preprocess it again).

iromeo commented 9 months ago

In this case - change BED format using Adjust BED Format action, save session & reload it.