Omar Abou Saada issues

Results 5 issues of


Omar Abou Saada

MAPQ of -2147483648 attributed to some reads in samfile (minimum value for an int32)

I'm using the following version of ngmlr: `ngmlr 0.2.7 (build: Jul 3 2020 03:31:03, start: 2020-07-19.14:10:32)` I ran the following command: `ngmlr -t 8 -x ont -r $reference -q $file.fastq.gz...

nPhase needs a guide/tutorial for working on large/very heterozygous genomes

As long as nPhase doesn't make efficient use of heuristics to drastically speed up prediction time, users will run into issues with trying to run it on large genomes and...

nPhase is too slow/memory intensive

Right now nPhase is deterministic, meaning it doesn't use any useful time-saving heuristics. It also makes no use of parallelization. Generally it isn't optimized. It would be good to work...

nPhase has no option to set max heterozygosity level

Whenever someone wants to run nPhase on a very heterozygous, large genome and runs into memory issues/takes too long to run, I recommend subsampling the vcf down to a 0.5~1%...

Running nphase partial with a .bam file or a .sam file that isn't sorted or has a header

Currently nphase partial fails if you don't provide the perfect formal for mapped longReads. I'll close this issue when I've updated it to automatically detect if the user submits a...