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seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
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Error on output on 'Not Found' variants #28

Closed nuin closed 5 years ago

nuin commented 5 years ago

Hi

We had a strange genome that had a bunch of Not found variants and when parsing the output from Haplogrep, the column in the line seems wrong as the listed variants have no separation among them

My_ID   1-16569;    L2d 0.9499  150T14845T16300G16354T  73G 146C 152C! 182T! 195C 263G 456T 750G 769A 870T 1018A 1438G 2159C 2332T 2416C 2706G 3254A 3434G 3594T 3693A 4104G 4769G 6231T 7028T 7256T 7521A 8206A 8701G 8860G 9221G 9540C 9554A 9941G 10115C 10398G 10873C 10955T 11353C 11719A 11944C 12705T 13590A 13650T 14766T 15301A 15326G 15777C 16189C 16223T! 16278T 16311C! 16390A 16399G  2362G 4048A 7868T 12487G 14007G 14010G 16189d   4048A [D248N| Codon 1 | ND1 ] 7868T [L95F| Codon 1 | COX2 ] 12487G [T51A| Codon 1 | ND5 ]   73G 146C 195C 263G 456T 750G 769A 870T 1018A 1438G 2159C 2332T 2362G 2416C 2706G 3254A 3434G 3594T 3693A 4048A 4104G 4769G 6231T 7028T 7256T 7521A 7868T 8206A 8701G 8860G 9221G 9540C 9554A 9941G 10115C 10398G 10873C 10955T 11353C 11719A 11944C 12487G 12705T 13590A 13650T 14007G 14010G 14766T 15301A 15326G 15777C 16189C 16189d 16278T 16390A 16399G

The problem is on the string

150T14845T16300G16354T

that should be 

150T 14845T 16300G 16354T

Thanks

nuin commented 5 years ago

Noticed that the latest version fixes that. Closing.