close file descriptor if cannot open gzFile
Uniqkmer command checks kmerkey values instead of just matching bkmers
Added ecoli correct examle and kmer-agnostic with error

1. Added ecoli example for read correction
2. Added script to download data for results
3. ctx_contigs.c, ctx_correct.c, ctx_coverage.c, ctx_exp_abc.c: Fixed memory
   calculation
4. src/tools/assemble_contigs.c fixed double counting of repeat ends
5. Started adding kmer agnostic tests for seqn with error
Fixed plotting of kmer_agnostic results
Remove kmer_agnostic tests without errors
Rename kmer_agnostic
Generate kmer-agnostic with stochastic coverage / error separately
Improvements to running and plotting stochastic covg+error [skip CI]
Clean up traversal conjecture Makefile [skip CI]
Change license GPL->MIT; Better cleaning statistics
Added lossless simulation with short reads
Move contig len hist to .ctp file header

Note: ctp files have changed and are not backwards compatible!
      We are now on CTP version 3.

Removed options to dump/load CSV of contig length histogram. This histogram
now lives in CTP path file headers.
Improve GraphWalker API

1. Improve GraphWalker API
2. Add ctx_contigs.c option to skip missing-info check when walking the graph
3. Run unit tests in tests/run.sh
Add 'pview' command; fix 'check' command; added --no-missing-check;

1. ctx_pview.c: Added pview command to print entire path

2. assemble_contigs.c: added option to assemle contigs using paths. Still has bugs

3. Fixed BUG in ctx_check.c where paths were not being checked

4. graph_walker.c: added option to not use missing info check

5. path_tests.c: Added tests to check paths are added properly
Fixed BUG in graph_walker.c:graph_walker_slow_traverse()

1. graph_walker.c: Fixed bug caused by not checking which edges were in the
   current colour in graph_walker_slow_traverse()
2. assemble_contigs.c: seeding with paths is now working
3. moved ContigStats assemble_contigs.c -> assemble_stats.c
ctp file header stores contig histogram for each colour
Use new model to pick cleaning threshold

1. pick cleaning threshold using Gil's model
2. print path sequence when seeding assemble_contigs.c
3. change kmer_occur.h limits to give max chroms = 2Billion, max chrom len = 4Gb
4. Fix issues found with clang's static analyzer
Replaced db_node_col_covg() with db_node_covg()
Removed oriented BinaryKmer (bkmer) from GraphWalker and simplified API
Improvements to path loading (.ctp files)

path loading:
a. handle loading subset of colours from multicolour paths file. This used to
   cause errors when a kmer was not in sample(s) being loaded
b. don't load all path colours -- use the filter!
c. check paths are not longer than longest contig in the header