Ilya Shlyakhter
Ilya Shlyakhter
Add option to create a kmer database from a simple text file listing the kmers and their counts, like what kmc_tools transform dump outputs. If counts are omitted, set them...
Add option to keep only reads containing a stretch of M _adjacent_ kmers at least N of which are in the database. This permits more flexible filtering than just using...
When filtering reads, with -ci0 for the reads (i.e. keep all reads, even ones with no kmers from the db), no hard-masking at all seems to happen. @marekkokot
Right now, a base is hard masked to N if at least 1 of the kmers it's in is "invalid" (has count less than -ci). Can you make that a...
The help message for hard masking says it masks "invalid" kmers. From other parts of kmc, I thought "invalid" means "count under -cx _or_ over -cx". But looking at the...
When constructing a kmer db from reads, sometimes I'm only interested in kmers that appear in another kmer db (e.g. kmers that have appeared in known genomes of taxon of...
@marekkokot Is there a test suite you use to verify correctness of kmc and kmc_tools? If there is, could it be checked into github?
The cutoff_max for a simple binary operation defaults to the higher cutoff_max of the operands. But for the union operation, the default way to combine the counters is SUM. This...
It'd be great to add an option to store for each kmer, instead of its count, the minimum or maximum position of that kmer in the input sequences. This would...
It's great that kmc now supports bam files input. Could you extend that to filtering reads? (For input and output).