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xyl012 claymcleod isabella232

squab's Issues

Example gff3 and bam file parsing works but strange behavior on gencode gff3

Hi,

Thanks for developing this cool tool. I came across perhaps an edge case that might be a difficult to debug with a gencode gff3 file. Unfortunately, I cannot share the BAM file, but what is strange is by accident, I got the command to work by using only the first few lines of the gff3

$ wget http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M27/gencode.vM27.annotation.gff3.gz
$ noodles-squab     --verbose     quantify     --annotations gencode.vM27.annotation.gff3.gz --output sample.counts.tsv Aligned.sortedByCoord.out.bam
Oct 11 09:15:45.764  INFO noodles_squab: using 24 thread(s)
Oct 11 09:15:45.767  INFO noodles_squab: reading features
Error: invalid attributes: invalid entry: empty input

$ noodles-squab     --verbose     quantify     --annotations <(zcat gencode.vM27.annotation.gff3.gz|head) --output sample.counts.tsv Aligned.sortedByCoord.out.bam
Oct 11 09:16:19.173  INFO noodles_squab: using 24 thread(s)
Oct 11 09:16:19.175  INFO noodles_squab: reading features
Oct 11 09:16:19.182  INFO noodles_squab: read 1 unique features
Oct 11 09:16:19.200  INFO noodles_squab::commands::quantify: detecting library type
Oct 11 09:16:19.324  INFO noodles_squab::commands::quantify: library layout: paired end
Oct 11 09:16:19.324  INFO noodles_squab::commands::quantify: strand specification: none (confidence: 0.00)
Oct 11 09:16:19.324  INFO noodles_squab::commands::quantify: counting features
Oct 11 09:16:19.909  INFO noodles_squab::commands::quantify: writing counts

$ cat sample.counts.tsv
ENSMUSG00000102693.2	0
__no_feature	178883
__ambiguous	0
__too_low_aQual	0
__not_aligned	0
__alignment_not_unique	24272

I am not sure what line of the gff3 is the culprit

Mismatch between definition and access of `min-mapping-quality`

Tried to use the latest version of squab quantify today and I got this issue. I was able to trace

$ squab quantify --output results.txt --annotations gencode.v41.annotation.gff3 $PATH_TO_BAM
thread 'main' panicked at 'Mismatch between definition and access of `min-mapping-quality`. Could not downcast to TypeId { t: _ }, need to downcast to TypeId { t: _ }

I was able to trace this back, it appears the issue was introduced in this commit: 4c24e8b. Do you get this when trying to run squab quantify

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