README.md

@@ -66,7 +66,7 @@ You can run resfinder command line using python3
 
 # Example of running resfinder
 python3 resfinder.py -i test.fsa -o . -p /path/to/resfinder_db \
--b /path/to/blastn -d aminoglycoside -k 90.00 -l 0.60
+-b /path/to/blastn -d aminoglycoside -t 0.90 -l 0.60
 
 # The program can be invoked with the -h option 
 Usage: resfinder.py [-h] [-i INPUTFILE] [-1 FASTQ1] [-2 FASTQ2] [-o OUT_PATH]
@@ -103,6 +103,10 @@ optional arguments:
   -t THRESHOLD, --threshold THRESHOLD
                         Blast threshold for identity
                         default minimum 0.9 
+  -matrix, --matrix
+                        If used, gives the counts all all called bases at each position
+                        in each mapped template. Columns are: reference base,
+                        A count, C count, G count, T count, N count, - count.
 ```
 
 ### Web-server

debian/changelog

-resfinder (3.1.0-1) UNRELEASED; urgency=medium
+resfinder (3.2-1) UNRELEASED; urgency=medium
 
   * Initial release (Closes: #<bug>)
   TODO: Clarify relation between *.pl and *.py
 
- -- Andreas Tille <tille@debian.org>  Thu, 18 Oct 2018 16:36:04 +0200
+ -- Andreas Tille <tille@debian.org>  Thu, 07 Nov 2019 12:41:11 +0100

debian/compat

-11

debian/control

@@ -3,8 +3,9 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 12),
+               dh-python
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/resfinder
 Vcs-Git: https://salsa.debian.org/med-team/resfinder.git
 Homepage: https://bitbucket.org/genomicepidemiology/resfinder
@@ -12,7 +13,7 @@ Homepage: https://bitbucket.org/genomicepidemiology/resfinder
 Package: resfinder
 Architecture: any
 Depends: ${perl:Depends},
-         ${python:Depends},
+         ${python3:Depends},
          ${misc:Depends},
          bioperl,
          ncbi-blast+-legacy

debian/upstream/metadata

@@ -14,3 +14,4 @@ Reference:
   URL: https://academic.oup.com/jac/article/67/11/2640/707208
   ePrint: >
     https://academic.oup.com/jac/article-pdf/67/11/2640/2085909/dks261.pdf
+Repository: https://git@bitbucket.org/genomicepidemiology/resfinder.git