Added perl scripts to parse/filter .ctp files [skip CI]
Add JSON headers to bubble and breakpoint caller output
Update command blurb
graph_files_merge() uses memory mapped files (mmap)
Memory mapping for ctx_infer_edges.c; Fix compilation issues

ctx_infer_edges.c:
- use memory mapped files when editing a file in place
- detect when reading from a stream by using stat()
- full suite of tests in tests/inferedges/Makefile

infer_edges.c:
- use either covgs or bitarray node_in_col to test if kmer in colour

Minor changes:

1. Convert comma operators to 'compound statements within expressions' (GNU C):
    e.g. ({ ctx_assert(); val; })
   This should fix compilation issues when asserts are turned off

2. Asserts+checks now turned off with `make RELEASE=1`
Test script [tests/run.sh] fetches dependencies before running
Set SHELL to bash in test Makefiles
Changed font used in graphviz (.dot) files
Fix error pulling out contigs with population

Fixes issue #5

1. Only use seed kmers that are in the sample we are pulling out contigs for
2. Allow pooling colours when checking sample names match
3. graph_file_reader.c, gpath_reader.c: paths are const char* not char* now
4. db_alignment.c: keep track of kmer origin position or -1 if inferred kmer
5. correct_alignment.c: operates on internal dBAlignment and takes reads as input
6. Print VCF header from JSON input headers
7. gpath_load_sample_pop() now won't complain if you give multi-colour graph file
   and only ask to load a single colour from it.
8. assemble_contigs.c: When pulling out a contig, give end status as HitRepeat
   if GraphWalker ok but RepeatWalker stopped.
Better graph edge check - runs per colour instead of union
Added alloc_flags arg to db_graph_alloc() for ease of use
Faster bkmer revcmp; Added `ctx31 sort`

1. faster binary_kmer_reverse_complement() function
2. better profiling of reverse complement code in dev/bkmer_revcmp
3. added `ctx31 sort` command for graph files, will add more options shortly
4. almost finished new read correction to fix bugs in indel/fastq outptut issues
Add command to run tests on graph traversal 'exp_ABC'
Got basic index command working
Add block size arguments to index command
Small improvements to sort/index commands
correct_reads.c using indel+qual safe code; Minor bug fixes.

0x0. cmd.c clones input arguments array

0x1. JSON header: better reporting of command line args - use array of strings
     instead of merging into a string without escaping spaces.

0x2. Print STDOUT/STDIN instead of "-" in lots of places.

0x4. scripts/seq2pdf.sh: fix some bugs when running not in scripts dir

0x8. Don't try to get file size when reading from STDIN ("-")

0x10. objbuf_macro.h: added FUNC_shift() function for shifting elements

0x20. ctx_exp_abc.c: report GraphWalker state at the end of traversals

0x40. util.c: added function util_print_nums() to report numbers nicely aligned

0x80. correct_reads.c: lots of work on correcting reads. Now using new version of
      code. Indels still not printing correctly though. Just a bit of tweaking
      required. Soon will handle indels and quality scores nicely.
Add script to mix path with graph kmers

1. gpath_reader.c: gpath_reader_load() takes int flag to define behaviour when
   we hit kmers that are not in the graph (add, die with error, or ignore)

Perl scripts:
1. CortexPaths.pm: add function ctp_path_to_str()
2. scripts/cortex_mix_paths.pl interweave kmers with their paths:

    $ ./scripts/cortex_mix_paths.pl --kmer 9 genome.k9.ctx <(zcat reads.pe.two.ctp.gz)
    CAGTGGCCG 1 1 ...t...T ...t...T
    R 5 1 1 A
    CACTGATGC 1 1 .c...C.. .c...C..
    CACTGATGA 1 1 .c...C.. .c...C..
    R 5 1 1 G
    TCGGCATCA 1 1 ......G. ......G.
    CGGCATCAG 1 1 ...t...T ...t...T
Added paths to cortex_to_graphviz.pl
cortex_to_graphviz.pl: mark given kmers