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jiantao / Tangram

Fast Structural Variation Detection Toolbox
MIT License
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tangram_detect: scaffold-based FASTA header not a valid reference name #6

Open frl1 opened 9 years ago

frl1 commented 9 years ago

Hi,

I am trying to run Tangram on a scaffold-based genome, named as scaffold1, scaffold2,... . However, when running tangram_detect with -rg set to "scaffold1" or left empty (to run on everything, is that possible?) I get: "ERROR: scaffold1 is not a valid reference name".

tangram_bam, tangram_index and tangram_scan went fine. As suggested in Issue #5, I used fake MD5 strings in the BAM header. Mapping was done in BWA.

I am grateful for any help.

Thanks, Fritjof