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tangerzhang / ALLHiC

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data
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The algorithm details about the ordering and orientations for contigs #14

Closed wlhCNU closed 5 years ago

wlhCNU commented 5 years ago

hi, I am very interested in algorithm details about the ordering and orientations for contigs. However the allhic is a binary code script. I want to get the readable code detail of the binary software to understand how the process of ordering and orientation is implemented. I would be very grateful if I can get your reply. Thanks.

tanghaibao commented 5 years ago

@wlhCNU

FYI - the source for the binary is here, and contains algorithm detail specifically in optimize.go. Paper is coming out soon too with a section on OO.

Haibao

wlhCNU commented 5 years ago 
   Thank you for you response. I still have a question to ask you. In the Tested data directory.  I found the content of draft.asm.fasta file is sam alignment formate. Is there a problem with the content of the file ?
   Thanks
tangerzhang commented 5 years ago

Hi @wlhCNU , did you download the test data from the following link (ftp://59.79.232.12/). I've just checked the draft.asm.fasta. It is fasta format rather than bam alignment. If there is still a problem, I can send you the file through email.

wlhCNU commented 5 years ago

Yes, I download the test data from the following link (ftp://59.79.232.12/). The data downloaded this time is correct. It may be that I made a mistake when I last downloaded the data. Sorry, it has caused you trouble. Thanks