diff --git a/README.md b/README.md index 53a530a..5051843 100644 --- a/README.md +++ b/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. diff --git a/mask.bed b/mask.bed index 4f324f7..732d29c 100644 --- a/mask.bed +++ b/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 \ No newline at end of file