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
GraphWalker: better tracking path age

Major change: Change how we traverse with paths
Change behaviour of GraphWalker to remember age of paths by when they were picked
up rather than how many junctions they have been used for. This seems to fix
the issues with the exp_abc simulations.

Minor:
ctx_exp_abc.c: add option to print failed contigs
ctx_supernodes.c: More changes to get ready to read in paths to print annotations
scripts/cortex_to_graphviz.pl: Bug fix when loading paths file
Fix bugs in reporting assembled contig stats
Use bioinf-perl module for formatting numbers
Remove debugging code; fix minor errors
Added example using contig_stats.pl
Improve FileFilter on input files

1. Update file filter syntax: <into>:file.ctx:<from> where <into> and <from> can
both be lists, ranges or empty. Examples:
 * 0,2,6-9:in.ctx:0-5  {0,1,2,3,4,5} -> {0,2,6,7,8,9}
 * 0:in.ctx:0,2,3      {0,2,3} -> {0,0,0}
 * in.ctx:0,1,3        {0,1,3} -> {0,1,2}

2. loading_stat.c:
  a. rename stats.contigs_loaded -> stats.contigs_parsed
  b. remove num_files_loaded, ctx_files_loaded, num_of_colours_loaded