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