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HongzheGuo / deBGA

de Bruijn Graph-based read aligner
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single-ended read option checking #4

Open fataltes opened 7 years ago

fataltes commented 7 years ago

Hi Hongzhe,

I think here : https://github.com/HongzheGuo/deBGA/blob/master/load_input.c#L583

the condition should be if(strcmp(argv[optind + 2] + strlen(argv[optind + 2]) - 3, ".fq") == 0 || strcmp(argv[optind + 2] + strlen(argv[optind + 2]) - 6, ".fastq") == 0)

to be able to run the "aln" command for single-ended reads.

HongzheGuo commented 7 years ago

Ye, the single-end read mapping mode starts here. However deBGA is mainly focused on the pair-end reads and it may not provide strong support for the single-end mapping.

fataltes commented 7 years ago

Alright. So then we have to go forward with pair-end reads. But it'll be great if you mention that specifically in you readMe that you no longer support single-end reads.

P.S. I still think maybe updating that line of the code could be useful.