8000 SAM file with corn leads to - is PAF a possibility ? · Issue #28 · eldariont/svim-asm · GitHub
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SAM file with corn leads to - is PAF a possibility ? #28
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SAM file with corn leads to - is PAF a possibility ?#28
@colindaven

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@colindaven
colindaven
opened on Dec 18, 2024

Hi,

thanks for this tool, it seems to work well and provide decent output for smaller genomes. When I look at MA at 2.3 GB, I get the following samtools error parsing the SAM CIGAR string. It seems PAF not SAM output is a better fit for this kind of tool.

[E::parse_cigar] CIGAR length too long at position 131

Are there any plans to use PAF instead of SAM in the future or are the CIGAR operators needed ?

Thanks

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