upgraded tests for read_fastq

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1786 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/read_fastq.in.1 b/bp_test/in/read_fastq.in.1
new file mode 100644 (file)
index 0000000..c070506
--- /dev/null
+++ b/bp_test/in/read_fastq.in.1
@@ -0,0 +1,8 @@
+@sanger
+aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
+@illumina1.8
+eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee
++
+!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ

diff --git a/bp_test/in/read_fastq.in.2 b/bp_test/in/read_fastq.in.2
new file mode 100644 (file)
index 0000000..99cfaa0
--- /dev/null
+++ b/bp_test/in/read_fastq.in.2
@@ -0,0 +1,12 @@
+@solexa
+bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
++
+;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@illumina1.3
+ccccccccccccccccccccccccccccccccccccccccc
++
+@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+@illumina1.5
+ddddddddddddddddddddddddddddddddddddddd
++
+BCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh

diff --git a/bp_test/in/read_fastq.in.2.gz b/bp_test/in/read_fastq.in.2.gz
new file mode 100644 (file)
index 0000000..77cce5e
Binary files /dev/null and b/bp_test/in/read_fastq.in.2.gz differ

diff --git a/bp_test/out/read_fastq.out.1 b/bp_test/out/read_fastq.out.1
index 4944eb402fa37065e52f0774293f3291d16d7edb..0d70eb8b4f02cbe24bb18047ce84bf8cd96c6e34 100644 (file)
--- a/bp_test/out/read_fastq.out.1
+++ b/bp_test/out/read_fastq.out.1
@@ -3,13 +3,8 @@ SEQ: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
 SEQ_LEN: 41
 SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
 ---
-SEQ_NAME: solexa
-SEQ: bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
-SEQ_LEN: 46
-SCORES: ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
----
-SEQ_NAME: illumina1.3
-SEQ: ccccccccccccccccccccccccccccccccccccccccc
-SEQ_LEN: 41
-SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+SEQ_NAME: illumina1.8
+SEQ: eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee
+SEQ_LEN: 42
+SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghi
 ---

diff --git a/bp_test/out/read_fastq.out.2 b/bp_test/out/read_fastq.out.2
index 11fa8ee0a35afc5777e0583dfec8d62d38cce1b6..a8451fbd4b5eb5517be1fd2436abe8622cbc4b07 100644 (file)
--- a/bp_test/out/read_fastq.out.2
+++ b/bp_test/out/read_fastq.out.2
@@ -1,5 +1,15 @@
-SEQ_NAME: sanger
-SEQ: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
+SEQ_NAME: solexa
+SEQ: bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
+SEQ_LEN: 46
+SCORES: ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+---
+SEQ_NAME: illumina1.3
+SEQ: ccccccccccccccccccccccccccccccccccccccccc
 SEQ_LEN: 41
 SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
 ---
+SEQ_NAME: illumina1.5
+SEQ: ddddddddddddddddddddddddddddddddddddddd
+SEQ_LEN: 39
+SCORES: BCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+---

diff --git a/bp_test/out/read_fastq.out.3 b/bp_test/out/read_fastq.out.3
index ae6f2a84259b6f3400e477216a25365fee85c28a..923c528d1dacd04fa40e7a087aa6dabd141f12c0 100644 (file)
--- a/bp_test/out/read_fastq.out.3
+++ b/bp_test/out/read_fastq.out.3
@@ -1,5 +1,5 @@
-SEQ_NAME: sanger
-SEQ: aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
-SEQ_LEN: 41
-SCORES: CCDDEFFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
+SEQ_NAME: solexa
+SEQ: bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
+SEQ_LEN: 46
+SCORES: ;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefgh
 ---

diff --git a/bp_test/test/test_read_fastq b/bp_test/test/test_read_fastq
index 0e3f3df0a2e91992593e424f2ca3d62fd0a4d1fe..6c597640c5880e7adbbafb473de478d20f8a9e5e 100755 (executable)
--- a/bp_test/test/test_read_fastq
+++ b/bp_test/test/test_read_fastq
@@ -2,18 +2,18 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -i $in -O $tmp"
+run "$bp -i $in.1 -O $tmp"
 assert_no_diff $tmp $out.1
 clean
 
-run "$bp -i $in.gz -O $tmp"
-assert_no_diff $tmp $out.1
+run "$bp -i $in.2 -O $tmp"
+assert_no_diff $tmp $out.2
 clean
 
-run "$bp -i $in -n 1 -O $tmp"
+run "$bp -i $in.2.gz -O $tmp"
 assert_no_diff $tmp $out.2
 clean
 
-run "$bp -i $in -n 1 -s -O $tmp"
+run "$bp -i $in.2 -n 1 -O $tmp"
 assert_no_diff $tmp $out.3
 clean