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nanoporetech / pinfish

Tools to annotate genomes using long read transcriptomics data
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error from spliced_bam2gff #7

Closed yuntwang closed 5 years ago

yuntwang commented 5 years ago

Hi when I use the command: ./spliced_bam2gff -s -t 10 -M data.sorted.bam >data.raw_transcripts.gff I get an error: **panic: runtime error: invalid memory address or nil pointer dereference [signal SIGSEGV: segmentation violation code=0x1 addr=0x40 pc=0x4cd426]

goroutine 1 [running]: main.SplicedBam2GFF(0x7fff21087b9a, 0x57, 0x52a9e0, 0xc420108008, 0xa, 0xc420108001, 0x2) /home/OXFORDNANOLABS/bsipos/gt/pinfish/spliced_bam2gff/bam2gff.go:29 +0xa6 main.main() /home/OXFORDNANOLABS/bsipos/gt/pinfish/spliced_bam2gff/main.go:22 +0x146** why? Hope to get your reply! Thanks

bsipos commented 5 years ago

Is the BAM file big? Is the data sensitive? If not, it would be useful if you could upload it somewhere and give access to it.

yuntwang commented 5 years ago

@bsipos I have found the reason that the header of bam is error.