Brian Walenz

Two reports. On a 3tb node: ``` p prefixes bits gigabytes (allowed: 1 GB) -- -------------- ---------------- --------- 21 2097152 76313443474 8.884 22 4194304 75010317320 8.732 23 8388608 73841408894 8.596...

steps for training

2

I like this approach to simulation; it lets me easily control the sequences simulated (e.g., letting me make chimeric reads, reads with garbage in the middle, etc) and, in theory,...

I split the existing CXXFLAGS into multiple lines, added a few -Wno options, and removed redundant -lpthread from the link. The rest of the changes are pretty simple. Compilation: -...

The prefixSize used for writing count output is too large when inputs are large too. https://github.com/marbl/meryl/blob/master/src/meryl/merylOp-countThreads.C#L404 Sets the output prefix based on the 'optimal' prefix used for counting. It works...

@arangrhie reports: ``` % meryl output read-$hap.1cp.meryl [ less-than $HI [ greater-than $LO read-$hap.meryl ] ] ``` works, but ``` meryl [ less-than $HI [ greater-than $LO read-$hap.meryl ] ]...

In 'print' output, it would be convenient to have the correct canonical kmer reported. Translate from ACTG to ACGT, recompute the canonical kmer, and output that. The output order will...

meryl cannot show a histogram on operations. ``` meryl histogram union-sum input1.meryl input2.meryl ERROR: operation 'opHistogram' can't take input from 'opUnionSum': it can only accept databases. ```

Allow changing the value of every kmer: ``` meryl add 1 [input] meryl mul 2 [input] meryl mul 2 add 1 [input] ```

cnspath mode doesn't create/copy all output files

1

Running verkko in `--paths` mode does not generate the same output files as a 'normal' run. The 'cnspath' rule does not create a `noseq.gfa` output - and probably others. This...