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brentp avatar brentp commented on May 23, 2024 1

here's a fix for that.
seqcover.gz

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oyvindbusk avatar oyvindbusk commented on May 23, 2024 1

Thanks, for the fix. No trouble at all!

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brentp avatar brentp commented on May 23, 2024

thanks. working on a fix for this now.

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oyvindbusk avatar oyvindbusk commented on May 23, 2024

Thanks, I seem to be getting the same error message even with the new binary you attached.

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brentp avatar brentp commented on May 23, 2024

I just download this file that I put here and ran:

~/Downloads/seqcover report --genes CCDC39    --fasta $fasta d4s/HG00*.d4

and it completes without problem. Are you sure you got this version?

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oyvindbusk avatar oyvindbusk commented on May 23, 2024

Ah, it works without the hg19-flag, but throws an error when hg19 is added.

./seqcover report --genes CCDC39 --fasta $fasta samples/1_50_recal.per-base.d4 --background seqcover_out/seqcover_p5.d4 -r my_genes_report.html
[seqcover] read 1 sample coverage files
res:{"query":"ENSG00000145075","_id":"ENSG00000145075","_version":1,"genomic_pos":{"chr":"3","end":180870933,"ensemblgene":"ENSG00000145075","start":180614008,"strand":-1},"name":"coiled-coil domain containing 39","symbol":"CCDC39","exons":[{"txstart":180614008,"txend":180870933,"cdsstart":180870933,"cdsend":180870933,"position":[],"chr":"3","transcript":"NA","strand":-1}]}
res:{"query":"339829","_id":"339829","_version":1,"exons":[{"cdsend":180679380,"cdsstart":180614920,"chr":"3","position":[[180614007,180615077],[180616280,180616363],[180616515,180616695],[180616825,180616966],[180619258,180619365],[180619810,180619970],[180631468,180631592],[180641992,180642201],[180644119,180644257],[180647078,180647243],[180648164,180648359],[180651400,180651533],[180652162,180652266],[180654761,180654953],[180659451,180659580],[180659676,180659769],[180660569,180660728],[180661860,180662007],[180663866,180663986],[180679290,180679489]],"strand":-1,"transcript":"NM_181426","txend":180679489,"txstart":180614007}],"genomic_pos":{"chr":"3","end":180684942,"ensemblgene":"ENSG00000284862","start":180602858,"strand":-1},"name":"coiled-coil domain containing 39","symbol":"CCDC39"}
3       180613507       180679989
[seqcover] wrote report to:my_genes_report.html
 ./seqcover report --genes CCDC39 --fasta $fasta samples/1_50_recal.per-base.d4 --background seqcover_out/seqcover_p5.d4  --hg19
[seqcover] read 1 sample coverage files
tables.nim(262)          []
Error: unhandled exception: key not found: exons_hg19 [KeyError]

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brentp avatar brentp commented on May 23, 2024

Hi, I have fixed that and several other cases as well. Sorry for the trouble, you're an early user, but we should be getting more stable soon. See attached binary for fixes.
seqcover.gz

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