Merge branch 'testing' into 'devel'

Merge testing into master

See merge request !6

.gitlab-ci.yml

@@ -4,4 +4,5 @@ build:
     - docker
   script:
     - pip install --upgrade pip setuptools wheel
-    - pip install '.'
+    - pip install cython numpy
+    - tox

README.md

@@ -135,11 +135,15 @@ technologies. E.g, when comparing a WES VCF file vs a SNP array, this
 tool can be quite useful.
 
 Output is a simple JSON file listing counts of concordant and discordant
-alleles. 
+alleles and some other metrics. It is also possible to output the discordant
+VCF records.
 
 Multisample VCF files are allowed; the samples to be evaluated have to be set 
 through a CLI argument.
 
+Variants from the `--call-vcf` are filtered to have a Genotype Quality (GQ) of
+at least 30 by default. This can be overruled by specifying `--min-qual 0`.
+The optional flag `--min-depth` can be used to set the minimum read coverage.
 
 #### Usage
 
@@ -154,10 +158,12 @@ Options:
                                 called multiple times  [required]
   -ps, --positive-samples TEXT  Sample(s) in positive-vcf to consider. May be
                                 called multiple times  [required]
-  -s, --stats PATH              Path to output stats json file  [required]
-  -dc, --discordant PATH        Path to output discordant VCF file
-  --help                        Show this message and exit
-  ```
+  -s, --stats PATH              Path to output stats json file
+  -dc, --discordant PATH        Path to output gzipped discordant vcf file
+  -mq, --min-qual FLOAT         Minimum quality of variants to consider
+  -md, --min-depth INTEGER      Minimum depth of variants to consider
+  --help                        Show this message and exit.
+```
 
 ## License