Isaac Turner

Add new command `query` to query sorted and indexed graphs on disk: ``` mccortex31 query [-k |-1 |-o out.ctx] ``` Output is either in the same format as `view` command...

Next version of the graph format should use a json header.

The breakpoint caller should mark kmers if they are used in a call. Unused kmers that are in a sample and not the referece ("novel kmers") should be used to...

Consider writing links to disk to reduce peak memory. Writing links to ~256 files, which can then be sorting and merged. Temporary file will look like: ``` ``` Sorting can...

The bubble caller has less power to assemble the reference allele vs sample allele since the reference colour is just a bag of kmers without link information. Reference sequences can...

Configure graph walking with a common argument across commands: -a,--assembly [missInfoCheck=T|F,minCumulConf=,minStepConf=] e.g. mccortex31 contigs --assembly missInfoCheck=F,minStepConf=0.99 graph.ctx > contigs.fa

When threading reads, a large amount of time is spent writing the link files (.ctp.gz) to disk. Currently the compression is single threaded. If many threads simultaneously compressed blocks in...

Implement: Waterman, M. S. & Eggert, M. (1987). "A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J. Mol. Biol. 197, 723–728. (http://www.ncbi.nlm.nih.gov/pubmed/2448477)