Improve seq2pdf.sh cmdline args; Add exp_abc Makefile
ctx31 correct: Fixed bugs in error correcting reads

Error correction of reads now works with insert/delete and base change sequening
errors. FASTQ quality scores are kept in phase with sequence.

tests/correct/Makefile: Added suitable tests which pass.

ctx_correct.c:
  added option to specify zero'd fastq quality character (-Z, --fq-zero)
Probability shouldn't ruin our tests
Update GWalker for new API; Slim down lookup3.h for binarykmers
Add traversal conjecture Makefile
Added contig confidences to GraphWalker; Cleaned up graph_walker.c

1. Added confidence calculation to GraphWalker
   * added tests in src/tests/graph_walker_tests.c
2. Moved GraphStep into seperate .c/.h files
3. moved db_graph_prev_nodes_with_mask() to db_graph.c from graph_walker.c
4. moved dna_bases_list_to_str() to dna.c from graph_walker.c
4. assemble_contigs.c prints contig confidences
5. Added new file format proposal
Forgot to add contig_confidence.{c,h}
Added scripts to re-run kmer-size analysis
Added steps to reproduce error correction test
Updated simulation makefiles [skip CI]
Reduce ctx-sort memory; rename readbuf_X() -> read_buf_X()
Bug fixes for ctx-sort and ctx-correct

BUG fixes:

1. Fix bug in ctx_sort.c for k > 31. We were not sorting by words after the first
   word in BinaryKmers.

2. ctx_sort.c should take the -f,--force command line option

3. correct_alignment.c was not setting aln->seq_gaps boolean properly. This was
   causing Ns in sequence to not trigger aln->seq_gaps to be true.

4. Try to get the username with getpwuid_r() if getlogin_r() fails

Improvements:

1. correct_reads.c: report number of gaps + num gaps filled

2. simplify db_alignment_print(aln) code - cleaner output for debugging
Added uniqkmers command

ctx_uniqkmers.c: `ctx31 uniqkmers` prints unique kmers. Useful for lossless
  storage of sequence where unique kmers are needed at flanks.

BUG FIXES

1. src/graph/binary_kmer.c: Fixed BUG in binary_kmer_random() function.
   rand() only returns 31 bits of random data, we were assuming it was 32.

2. Fix tests which were assuming binary_kmer_random() was returning kmer-keys
Fix BUG: undefined behaviour for k=33
Forgot to add ctx_uniqkmers.c file
Fix BUG in dna_revcomp_str() and merge similar functions
Dump contig size distributions with ctx_thread.c

ctx_thread.c and ctx_correct.c can now dump contig size distributions

ctx_join.c: Fix BUG in joining files that do not require loading the whole graph
contig confidence given threaded distribution

ctx_thread.c can now dump csv of read lengths - only stored if dump requested
ctx_contigs.c can now load csv and calculate confidence table from it
Fixed uniqkmers to properly add unique flanking kmers. Added lossless test.
Try using master branch on htslib/bcftools/samtools