From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d> Date: Tue, 10 Apr 2012 19:03:10 +0000 (+0000) Subject: upgraded tests for read_fastq X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=8d721ab5f7a6d9f8de388dc9720eb6a430ea10bf;p=biopieces.git 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 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 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 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 4944eb4..0d70eb8 100644 --- 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 11fa8ee..a8451fb 100644 --- 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 ae6f2a8..923c528 100644 --- 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 0e3f3df..6c59764 100755 --- 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