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entries in FASTA not listed in order #1489
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Noted. How is your genome specified, by json, .genome, or are you just loading a fasta? The order in the fasta has never been the only determinate, many fastas are alphabetical and have chr11 before chr2 for example. |
I load my genomes as a fasta. I name my genomes such to avoid this problem, so that they are both alphabetically named and placed in that order in the fasta. So with 2.16.0 the displayed view was the same as the order in the fasta, now with 2.17.2 it is random. Here is the same genome.fasta loaded into 2.16.0 so something has changed |
I think the same order as the FASTA would be the expected behavior. Ideally folks put it in the order they want it. |
Yes noted, definitely something has changed. Consider it a bug. Most folks are not creating their own fastas, they are just loading them from a repository, but I agree if you are creating your own that would be the expected behavior. I will fix it for the next point release. BTW technically the order in the fasta never controlled this, it was the order in the index (fai) file. I would rearrange the order of the index entries, which is much easier than rearranging the order in a large fasta such as human. That is the behavior I will restore. When using ".json" format you can specify the order in a property. The deprecate ".genome" format had a flag to control this. |
OK, sounds good. thanks. In this case the fai index has the same order as the fasta so I wonder how they are being re-arranged in the latest version? Chr01A 78365069 8 100 101 |
Sorry if I've not been clear, this has changed in the latest version, as I said consider it a bug. I was referring to previous versions. At the moment you can continue to use 2.16 until the next point release, probably early March, or alternatively wait until this is fixed in the development build. I will update here when a fix is available in the development build. |
I see. Thanks! |
If you are curious about sorting you can follow the logic here. I think the leading zero in your numeric names might be throwing this off (07 vs 7), but I'm not sure. In any event I'll restore the previous behavior if loading directly from a fasta. https://github.com/igvteam/igv/blob/master/src/main/java/org/broad/igv/feature/genome/ChromosomeComparator.java |
2.17.3 and 2.17.4 still have this problem |
@zongzone What problem exactly? |
entries in FASTA not listed in order |
OK, I don't see a fix for this released, its still open. This will be closed when there is a fix, hopefully soon. |
this is a difference between 2.16.0 and 2.17.2 (haven't checked in-between). The order of chromosomes is not the same as in FASTA or even alphabetical. It appears random?
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