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update list of changes
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katholt committed Mar 15, 2016
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6 changes: 4 additions & 2 deletions README.md
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Updates in master branch, to be in next release

1. /data directory includes files for subtyping of the LEE pathogenicity island of E. coli, as per [Ingle et al, 2016, Nature Microbiology](http://www.nature.com/articles/nmicrobiol201510). [Instructions below](https://github.com/katholt/srst2#typing-the-lee-pathogenicity-island-of-E-coli)
1. /data directory includes files for subtyping of the LEE pathogenicity island of E. coli, as per [Ingle et al, 2016, Nature Microbiology](http://www.nature.com/articles/nmicrobiol201510). [Instructions below](https://github.com/katholt/srst2#typing-the-lee-pathogenicity-island-of-e-coli)

2. Fixed ARGannot.r1.fasta to include proper mcr1 DNA sequence
2. Resistance gene database updates:
- Fixed ARGannot.r1.fasta to include proper mcr1 DNA sequence.
- Added columns to the ARGannot_clustered80.csv table, to indicate classes of beta-lactamases included in the ARGannot.r1.fasta database according to the [NCBI beta-lactamase resource](http://www.ncbi.nlm.nih.gov/pathogens/beta-lactamase-data-resources/) (new location for the Lahey list).

3. Fixed some issues with handling of missing data (i.e. where there were no hits to MLST and/or no hits to genes) when compiling results into a table via --prev_output. This could result in misalignment of gene columns in previous versions.

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