Gap2Seq
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rikuu
Gap2Seq is a gap filling and insertion genotyping tool.
Cut 71 scaffolds into 71 contigs and 0 gaps Traceback (most recent call last): File "./Gap2Seq", line 445, in args['bed'], args['gaps'] = cut_gaps(args['k'], args['fuz'], args['mask'], args['scaffolds']) File "./Gap2Seq", line 311,...
@rikuu would it be possible to tag a release, that includes the bugfixes since 3.1? also, to upload to github, as part of the release, a tarball that includes the...
Hi! I used Gap2Seq to fill gaps of my samples, but when running Gap2seq, I can't get any outputs. Then I tried the Gage exsample, also didn't get outputs. I...
at https://github.com/rikuu/Gap2Seq/blob/master/src/Gap2Seq.py#L497 if no gaps are filled, then tmp.filled is not created then https://github.com/rikuu/Gap2Seq/blob/master/src/Gap2Seq.py#L504 fails. @rikuu
Hi every one, I installed the program Gap2Seq, and I found different bugs (or I hope) in the binary Gap2Seq. when you ran the Gap2Seq like this: Gap2Seq --vcf insertions_filtered.vcf...
Dear, I only want to know which format return the program... I ran several programs to detect de novo insertions, but I want to know if the vcf which I...
Hey, I've been testing Gap2Seq's insertion genotyping ability, by randomly inserting "gaps" (replacing nucleotides in the fasta reference). 1. The results were rather impressive, as it can even fill gaps...
Upon running this line of code while installing Gap2Seq: cd thirdparty/htslib; make; cd .. I generate the below 'fatal error': gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc...
Hi, Gap2Seq looks like a great tool and mostly performed well when I tested it (closing most smaller [
