adds test for najoshi#32

idiv-biodiversity · Aug 13, 2014 · 80c85ff · 80c85ff
1 parent 8ae84f4
commit 80c85ff
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Showing 4 changed files with 33 additions and 2 deletions.
diff --git a/test/Makefile.am b/test/Makefile.am
@@ -1,6 +1,6 @@
-TESTS = sickle-se-success.sh sickle-pe-success.sh sickle-pe-memcheck.sh sickle-se-memcheck.sh
+TESTS = sickle-se-success.sh sickle-pe-success.sh sickle-pe-memcheck.sh sickle-se-memcheck.sh segfault-on-empty-reads.sh
 
-EXTRA_DIST = $(TESTS) test.fastq test.f.fastq test.r.fastq
+EXTRA_DIST = $(TESTS) test.fastq test.f.fastq test.r.fastq segfault-on-empty-reads-1.fastq segfault-on-empty-reads-2.fastq
 
 TEST_EXTENSIONS = .sh
 SH_LOG_COMPILER = bash -x
diff --git a/test/segfault-on-empty-reads-1.fastq b/test/segfault-on-empty-reads-1.fastq
@@ -0,0 +1,8 @@
+@HISEQ:140:H9N47ADXX:1:1101:1200:2194 1:N:0:TCCTGAGCTATCCTCT
+TATCAACGCAGAGTAC
++
+8??DDD86:F1??AEF
+@HISEQ:140:H9N47ADXX:1:1101:1596:2197 1:N:0:TCCTGAGCTATCCTCT
+TATCAACGCAGAGTAC
++
+CCCFFFFFHHGHHHGH
diff --git a/test/segfault-on-empty-reads-2.fastq b/test/segfault-on-empty-reads-2.fastq
@@ -0,0 +1,8 @@
+@HISEQ:140:H9N47ADXX:1:1101:1200:2194 2:N:0:TCCTGAGCTATCCTCT
+
++
+
+@HISEQ:140:H9N47ADXX:1:1101:1596:2197 2:N:0:TCCTGAGCTATCCTCT
+GTGGAAACAACACAGAGATCACCTTGCCCC
++
+0-(-(:)8>?8((<(:)).9>7><?);>?<
diff --git a/test/segfault-on-empty-reads.sh b/test/segfault-on-empty-reads.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+FILE_O=$(mktemp)
+FILE_P=$(mktemp)
+FILE_S=$(mktemp)
+
+trap "rm -f $FILE_O $FILE_P $FILE_S" EXIT
+
+../src/sickle pe \
+  -t illumina \
+  -f "$(dirname "$0")"/segfault-on-empty-reads-1.fastq \
+  -r "$(dirname "$0")"/segfault-on-empty-reads-2.fastq \
+  -o $FILE_O \
+  -p $FILE_P \
+  -s $FILE_S