Merge branch 'master' into tbdb

README.md

@@ -18,13 +18,13 @@ If you think a mutation should be removed or added please raise and issue [here]
 If you want to help curate the library, leave a comment [here](https://github.com/jodyphelan/tbdb/issues/4).
 
 #### Adding/removing mutations
-Mutations can be added by submitting a pull request on a branch modified `tbdb.csv` file. If that previous sentence made no sense to you then you can suggest a change using an [issue](https://github.com/jodyphelan/tbdb/issues) and we will try help. On submitting a pull request the `tbdb_bot` will automatically calculate the confidence of the mutations in question and submit the results as a comment on the pull request (like [this](https://github.com/jodyphelan/tbdb/pull/5)). All `tbdb_bot` checks should pass, at least two reviews should be requested and upon review can be merged into the master branch
+Mutations can be added by submitting a pull request on a branch modified `mutations.csv` file. If that previous sentence made no sense to you then you can suggest a change using an [issue](https://github.com/jodyphelan/tbdb/issues) and we will try help. On submitting a pull request the `tbdb_bot` will automatically calculate the confidence of the mutations in question and submit the results as a comment on the pull request (like [this](https://github.com/jodyphelan/tbdb/pull/5)). All `tbdb_bot` checks should pass, at least two reviews should be requested and upon review can be merged into the master branch
 
 ## How does it work?
 
-The mutations are listed in [tbdb.csv](https://github.com/jodyphelan/tbdb/blob/master/tbdb.csv). These are parsed by `parse_db.py` to generate the json formatted database used by TBProfiler along with a few more files. Mutations can be removed and added from tbdb.csv and a new library can be built using `parse_db.py`.
+The mutations are listed in [mutations.csv](https://github.com/jodyphelan/tbdb/blob/master/mutations.csv). These are parsed by `parse_db.py` to generate the json formatted database used by TBProfiler along with a few more files. Mutations can be removed and added from mutations.csv and a new library can be built using `parse_db.py`.
 
-#### tbdb.csv
+#### mutations.csv
 This is a CSV file which must contain the following column headings:
 1. **Gene** - These can be the gene names (e.g. *rpoB*) or locus tag (e.g. *Rv0667*).
 2. **Mutation** - These must follow the [hgvs nomenclature](http://varnomen.hgvs.org/). More info down below.

mask.bed

@@ -51,9 +51,7 @@ Chromosome	99162	99174
 Chromosome	102100	102138
 Chromosome	102140	102150
 Chromosome	103743	103756
-Chromosome	103788	104164
-Chromosome	104317	104985
-Chromosome	104986	104987
+Chromosome	103788	104987
 Chromosome	106207	106343
 Chromosome	125830	125834
 Chromosome	126259	126260
@@ -2289,4 +2287,4 @@ Chromosome	4379044	4379049
 Chromosome	4383144	4383145
 Chromosome	4385743	4385744
 Chromosome	4400660	4400663
-Chromosome	4411494	4411532
+Chromosome	4411494	4411532