added test_read_solexa to tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1034 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/read_solexa.in b/bp_test/in/read_solexa.in
new file mode 100644 (file)
index 0000000..9aff44f
--- /dev/null
+++ b/bp_test/in/read_solexa.in
@@ -0,0 +1,12 @@
+@HWI-EAS157_20FFGAAXX:2:1:888:434
+TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG
++HWI-EAS157_20FFGAAXX:2:1:888:434
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe
+@HWI-EAS157_20FFGAAXX:2:1:898:373
+TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT
++HWI-EAS157_20FFGAAXX:2:1:898:373
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh
+@HWI-EAS157_20FFGAAXX:2:1:907:487
+TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT
++HWI-EAS157_20FFGAAXX:2:1:907:487
+hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh

diff --git a/bp_test/out/read_solexa.out.1 b/bp_test/out/read_solexa.out.1
new file mode 100644 (file)
index 0000000..4d8747c
--- /dev/null
+++ b/bp_test/out/read_solexa.out.1
@@ -0,0 +1,15 @@
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe
+SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh
+SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh
+SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487
+---

diff --git a/bp_test/out/read_solexa.out.2 b/bp_test/out/read_solexa.out.2
new file mode 100644 (file)
index 0000000..a228e53
--- /dev/null
+++ b/bp_test/out/read_solexa.out.2
@@ -0,0 +1,5 @@
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe
+SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
+---

diff --git a/bp_test/out/read_solexa.out.3 b/bp_test/out/read_solexa.out.3
new file mode 100644 (file)
index 0000000..f6edd43
--- /dev/null
+++ b/bp_test/out/read_solexa.out.3
@@ -0,0 +1,15 @@
+SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;11;40;37;
+SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGTGG
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
+---
+SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;39;40;16;40;
+SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATAT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373
+---
+SCORES: 40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;40;27;40;40;40;
+SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487
+---

diff --git a/bp_test/out/read_solexa.out.4 b/bp_test/out/read_solexa.out.4
new file mode 100644 (file)
index 0000000..d0eb23c
--- /dev/null
+++ b/bp_test/out/read_solexa.out.4
@@ -0,0 +1,15 @@
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe
+SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGtGG
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh
+SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATaT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh
+SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGATTT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487
+---

diff --git a/bp_test/out/read_solexa.out.5 b/bp_test/out/read_solexa.out.5
new file mode 100644 (file)
index 0000000..c389c26
--- /dev/null
+++ b/bp_test/out/read_solexa.out.5
@@ -0,0 +1,15 @@
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhe
+SEQ: TTGGTCGCTCGCTCCGCGACCTCAGATCAGACGtGG
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:888:434
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhghPh
+SEQ: TTCTTGTTGTTGAAATACAACGATGGTTTTTCATaT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:898:373
+---
+SCORES: hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[hhh
+SEQ: TGAATGCCTGGGAGGAGTCCCGGAGTGTAGAGaTTT
+SEQ_LEN: 36
+SEQ_NAME: HWI-EAS157_20FFGAAXX:2:1:907:487
+---

diff --git a/bp_test/test/test_read_solexa b/bp_test/test/test_read_solexa
new file mode 100755 (executable)
index 0000000..63a1ad0
--- /dev/null
+++ b/bp_test/test/test_read_solexa
@@ -0,0 +1,23 @@
+#!/bin/bash
+
+source "$BP_DIR/bp_test/lib/test.sh"
+
+run "$bp -i $in -O $tmp"
+assert_no_diff $tmp $out.1
+rm $tmp
+
+run "$bp -i $in -n 1 -O $tmp"
+assert_no_diff $tmp $out.2
+rm $tmp
+
+run "$bp -i $in -c -O $tmp"
+assert_no_diff $tmp $out.3
+rm $tmp
+
+run "$bp -i $in -s -O $tmp"
+assert_no_diff $tmp $out.4
+rm $tmp
+
+run "$bp -i $in -s -C 30 -O $tmp"
+assert_no_diff $tmp $out.5
+rm $tmp

diff --git a/code_ruby/Maasha/lib/biopieces.rb b/code_ruby/Maasha/lib/biopieces.rb
index 171136b854217bc2ed159e7d0f33604b24915b59..f2776f2da4411c6ac98e47577cdf3aa37ef2e6a1 100644 (file)
--- a/code_ruby/Maasha/lib/biopieces.rb
+++ b/code_ruby/Maasha/lib/biopieces.rb
@@ -623,7 +623,7 @@ def do_at_exit(exit_status="OK-martin")
       FileUtils.remove_entry_secure(status.get_tmpdir)
       status.log(exit_status)
       status.delete
-      puts "EXIT STATUS: #{exit_status}"
+      puts "DEBUG EXIT STATUS: #{exit_status}" # DEBUG
     end
   end
 end