…uded. minor update to .gitignore.

…y minor comments and syntax updates to fileutil.

…ecord_and_detect_IUPAC. Default for base shred method set to true, so warnings are enables across .fa/.fq files. Default set to True throughout, so no question there. Default invocation (therefore suppressed) produces single warning for iupac module. 'Standard sequence' warning deprecated, it's lousy information. 789ish lines added. Adds/changes graph.py, __init__.py for edge graph creation 'graph' command. Bump version. Closes #123.

On other note, version bump for first inclusion of the graph structure into disk and memory. Beginning alternate pipeline of commands for assembly.

If i'm honest, the whole codebase needs a one over. Issue #124.

…ersion bumps, massive issues in __init__ graph.py kmer.py util.py. Refactor logging symmetry issues could spill over in fileutil if possible.

graph, __init__, kmer, util function abstractions, kmer.neighbor, logging changes, neighbor vs adjacency, pairs, new_type1_ids, new_type2_ids, char_first, char_last

Creating masthead and usage notes for graph, but there's a lot of files and stats to keep track of.

I'm introducing the plan for the file "quick_stats.txt"

A summary file that provides tabular per-file k-mer counts, with associated metadata

I'm also at a comfortable state of the edge list generation loops.

There's a lot to be done and I don't know how much to document vs trusting in the intuitive nature of the interface.

Still working on personal issues, 20-30h work.

Honest assessment of myself.

…e board, version bump to v0.7.8. In this commit, tested on Cdiff_R3.fa (in test/data), the graph subcommand produces a valid metadata header, and writes the outputs to stdout and to the .kdbg file, and correctly asserts/validates the relationship between unique k-mers, unique nullomers, and the number of theoretically possible k-mers.

….fq files with improved logging, logs a warning about the observed inconsistencies and note about plausible origin from .fa/.fq input.

…Parser class into the parse submodule. wakka wakka!