Added more tests

tseemann · Aug 3, 2017 · 83e43b2 · 83e43b2
1 parent 86cbd69
commit 83e43b2
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Showing 6 changed files with 12 additions and 4 deletions.
diff --git a/VelvetOptimiser.pl b/VelvetOptimiser.pl
@@ -2,7 +2,7 @@
 #
 #       VelvetOptimiser.pl
 #
-#       Copyright 2008, 2009, 2010 Simon Gladman <simon.gladman@monash.edu>
+#       Copyright 2008, 2009, 2010 Simon Gladman <simon.gladman@unimelb.edu.au>
 #
 #       This program is free software; you can redistribute it and/or modify
 #       it under the terms of the GNU General Public License as published by

diff --git a/test/data/test_long_R1.fq.gz b/test/data/test_long_R1.fq.gz
diff --git a/test/data/test_long_R2.fq.gz b/test/data/test_long_R2.fq.gz
diff --git a/test/mutant_R1.fastq.gz → test/data/test_short_R1.fq.gz b/test/mutant_R1.fastq.gz → test/data/test_short_R1.fq.gz
diff --git a/test/mutant_R2.fastq.gz → test/data/test_short_R2.fq.gz b/test/mutant_R2.fastq.gz → test/data/test_short_R2.fq.gz
diff --git a/test/run_test.sh b/test/run_test.sh
@@ -1,13 +1,21 @@
 #!/bin/bash
 
-echo "Running VelvetOptimiser on test data."
+echo "Running VelvetOptimiser on short test data."
 
-VelvetOptimiser.pl -s 55 -e 59 -f "-shortPaired -fastq.gz -separate mutant_R1.fastq.gz mutant_R2.fastq.gz" -d test_out
+VelvetOptimiser.pl -s 55 -e 59 -f "-shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz" -d test_out
 
 echo "Number of contigs in final assembly:"
 
 grep -c ">" test_out/contigs.fa
 
+echo "Running VelvetOptimiser on short and long test data."
+
+VelvetOptimiser.pl -s 43 -e 91 -x 4 -f "-shortPaired -fastq.gz -separate data/test_short_R1.fq.gz data/test_short_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz" -d test_out_2 -o "-long_mult_cutoff 3"
+
+echo "Number of contigs in final assembly:"
+
+grep -c ">" test_out_2/contigs.fa
+
 echo "Estimation of memory test:"
 
-VelvetOptimiser.pl -s 55 -e 59 -f "-shortPaired -fastq.gz -separate mutant_R1.fastq.gz mutant_R2.fastq.gz" -g 0.2
+VelvetOptimiser.pl -s 55 -e 59 -f "-shortPaired -fastq.gz -separate mutant_R1.fq.gz mutant_R2.fq.gz -longPaired -fastq.gz -separate data/test_long_R1.fq.gz data/test_long_R2.fq.gz" -g 0.2