Merge pull request #2 from ncbi/dev

Some  cosmetic improvements, no change in software.

.github/workflows/linux-cpp.yml

@@ -3,7 +3,6 @@ name: Linux C++ CI
 on:
   workflow_dispatch:
   push:
-  pull_request:
 
 jobs:
   build:

.github/workflows/mac-cpp.yml

@@ -3,7 +3,6 @@ name: MacOS C++ CI
 on:
     workflow_dispatch:
     push:
-    pull_request:
 
 jobs:
     build:

README.md

@@ -76,8 +76,8 @@ The output of StxTyper is a tab-delimited file with the following fields, all pe
       terminating at contig boundaries
     - __PARTIAL_CONTIG_END__ for partial operons that could be split by contig
       boundaries due to sequencing or assembly artifacts
-    - __EXTENDED__ Where the coding sequence would extend beyond the stop codon
-      for the reference protein
+    - __EXTENDED__ The coding sequence extends beyond the reference stop codon
+      for one or both of the reference proteins
     - __INTERNAL_STOP__ for Stx operons where one of the subunits has a
       nonsense mutation
     - __FRAMESHIFT__ where StxTyper detected an indel in the coding sequence

test_stxtyper.sh

@@ -46,31 +46,6 @@ function test_input_file {
     fi
 }
 
-function test_amrfinder_output {
-    local test_base=$1
-    if ! $STXTYPER --amrfinder -n "test/$test_base.fa" > "test/$test_base.amr.got"
-    then
-        echo "not ok: $STXTYPER returned a non-zero exit value indicating a failure of the software"
-        echo "#  $STXTYPER -n test/$test_base.fa > test/$test_base.amr.got"
-        return 1
-    else
-        if ! diff -q "test/$test_base.amr.expected" "test/$test_base.amr.got"
-            ###### STOPPED HERE ######
-        then
-            echo "not ok: $STXTYPER returned output different from expected"
-            echo "#  $STXTYPER -n test/$test_base.fa > test/$test_base.got"
-            echo "# diff test/$test_base.expected test/$test_base.got"
-            diff "test/$test_base.expected" "test/$test_base.got"
-            echo "#  To approve run:"
-            echo "#     mv test/$test_base.got test/$test_base.expected "
-            return 1
-        else
-            echo "ok: test/$test_base.fa"
-            return 0
-        fi
-    fi
-}
-
 
 test_input_file 'basic'
 FAILURES=$(( $? + $FAILURES ))