Re: Regarding LoRTIA

[Andrius Merkys <merkys@debian.org>]

Hello,

On 2020-11-01 18:59, shruti gupta wrote:
> shruti@debian:~/LoRTIA$ LoRTIA -5 AGAGTACATGGG --five_score 16
> --check_in_soft 15 -3 AAAAAAAAAAAAAAA --three_score 18 -s poisson -f
> True ./test/test.sam ./output/ ./test/test_reads.fasta
> Sorting ./test/test.sam...
> Iterating over ./test/test.sam...
> Generating statistics...
> Sorting and indexing output...
> Counting coverage...
> Processed files saved to ./output/
>
> Calculating l3 feature statistics...
> Calculating r3 feature statistics...
> Calculating r5 feature statistics...
> Feature file ./output//test_r5.tsv is empty. There is nothing to do here.
> Calculating l5 feature statistics...
> Feature file ./output//test_l5.tsv is empty. There is nothing to do here.
> Calculating in feature statistics...
> ERROR: The specified reference file does not contain contigs          
>     from the references used for mapping. Supply the same reference  
>            that was used for the mapping and try again.

Looks like LoRTIA encountered an error. Is this a sample input coming
from the LoRTIA upstream package? I would expect it to pass without
errors, but maybe the upstream has added this test to demonstrate the
limitations. Anyway I would suggest examining the situation before
moving with the further packaging of LoRTIA.

Best,
Andrius