Tests: add tests for the CLI

.gitlab-ci.yml

@@ -17,9 +17,12 @@ build:
 
 test:
   stage: test
+  before_script:
+    - apt install -y zutils diffutils
   script:
     - cd tests
     - ./test_bam
     - ./test_read_file
+    - ./tests.sh
 
   

tests/data/expected_list

+1	10
+A	11

tests/data/expected_range

+1	2	6	6
+1	0	1	1
+1	9	10	0
+A	0	1	0
+A	8	11	2

tests/data/expected_range_bed

+A	5	6	1
+A	6	7	2
+A	7	8	2
+A	8	9	0
+A	9	10	2

tests/data/expected_whole_bed

+1	0	10	6
+A	0	11	5

tests/tests.sh

+#!/bin/bash
+set -e
+
+INDEX=$(tempfile)
+../coverind index -b $INDEX data/test1.bam
+
+RESULTS=$(tempfile)
+../coverind query -l -i $INDEX > $RESULTS
+diff $RESULTS data/expected_list
+
+(
+    ../coverind query -i $INDEX -r 1:2-5
+    ../coverind query -i $INDEX -r 1:0-0
+    ../coverind query -i $INDEX -r 1:9-9
+    ../coverind query -i $INDEX -r A:0-0
+    ../coverind query -i $INDEX -r A:8-10
+) > $RESULTS
+diff $RESULTS data/expected_range
+
+../coverind query -i $INDEX -b $RESULTS
+diff <(zcat $RESULTS) data/expected_whole_bed
+
+../coverind query -i $INDEX -b $RESULTS -w 1 -r A:5-9
+diff <(zcat $RESULTS) data/expected_range_bed
+
+rm -f $RESULTS $INDEX*
+