Sanger Pathogens Iva Versions Save

Triggered to sync up latest version with conda

• Fix failing travis and docker hub build

bug fix: iva_qc crashes on a reference genome with no CDS. Fix added to stop iva_qc_make_db from including anthing without at least one CDS.

Require Pysam version to be at least 0.8.1 (previously also had to be <=0.8.3 because of pyasm build issues).

Two little changes, which won't affect results.

1. Highlight the --reference option as experimental.
2. added Travis CI.

Add support for new samtools sort syntax introduced in 1.2. Keep support for old samtools versions as well.

• force to use pysam 0.8.1-0.8.3. The new 0.9.0 will not install.

Now runs kmc in multi-threaded mode by default. To force kmc to use one thread, use the new option --kmc_onethread.