Thanks so much for developing this tool. I'm currently exploring the usage of yak to see if I could incorporate it into a pipeline. In the pipeline, I'd need to get a list a kmers (preferably one I could read). To to this with yak,
I tried to use yak to generate a list of kmers via these two commands:
""
./yak count -b37 -t6 -o kmers.yak reads.fq.gz
./yak inspect -p kmers.yak > list.kmers
""
However, the output is the exact same as the command to develop a histogram, i.e.
"
./yak inspect kmers.yak > list.kmers
Admittedly, "./yak inspect -h" only presents a single flag "-m" for use, which perhaps means that "-p" has been discontinued? Am I misunderstanding what the program is supposed to be doing (highly likely), or is this a bug? Please advise.
Hi Dr. Li,
Thanks so much for developing this tool. I'm currently exploring the usage of yak to see if I could incorporate it into a pipeline. In the pipeline, I'd need to get a list a kmers (preferably one I could read). To to this with yak,
I downloaded the latest branch: " git clone https://github.com/lh3/yak.git cd yak && make "
I tried to use yak to generate a list of kmers via these two commands: "" ./yak count -b37 -t6 -o kmers.yak reads.fq.gz ./yak inspect -p kmers.yak > list.kmers ""
However, the output is the exact same as the command to develop a histogram, i.e. " ./yak inspect kmers.yak > list.kmers
HS 1023 0 139628 139628 HS 1022 0 140 139768 HS 1021 0 149 139917 HS 1020 0 137 140054 HS 1019 0 160 140214 HS 1018 0 120 140334 HS 1017 0 129 140463 "
Admittedly, "./yak inspect -h" only presents a single flag "-m" for use, which perhaps means that "-p" has been discontinued? Am I misunderstanding what the program is supposed to be doing (highly likely), or is this a bug? Please advise.
Thanks in advance! Best, bjp