Version 0.4.1

SPAdes option changed from --trusted-contigs to --untrused-contigs, so that it doesn't output contigs that are not present in the reads

Version 0.4.0

• added an option to skip running cd-hit
• new flag for when a contig has >1 match to gene, but hits are on opposing strands

Version 0.3.2

Bug fix: sometimes there is zero read depth ina contig at a position where a variant was called by comparing contig to reference gene. This was causing ARIBA to crash.

Version 0.3.1

Bug fixes:

• stop trying to give SSPACE s.d. >1
• don't run local assembly when closest gene in cluster not found (usually becuase not enough reads in the cluster)
• there was an error getting read depth at indels

Version 0.3.0

• more columns in output
• use bowtie2 instead of smalt
• sspace/gapfiller optional
• sanity check input genes fasta

Version 0.2.0

Cluster reads before assembling. Use closest gene from each cluster to aid local assembly.

Tidy up verbose output

Clean up output directory automatically

Version 0.1.2

Use SPAdes instead of Velvet by default.
Better handling of paths to external programs.

Version 0.0.1

Merge pull request #1 from martinghunt/master

Initial working version