updated tests for read_sff

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1270 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/out/read_sff.out.1 b/bp_test/out/read_sff.out.1
index 299cfe32fcdb18724cf2aa1b77f1ef6711fcffc9..ed88d7c0b57cc738a1006533ad27ebedcc4ab867 100644 (file)
--- a/bp_test/out/read_sff.out.1
+++ b/bp_test/out/read_sff.out.1
@@ -3,88 +3,108 @@ SEQ: TCAGTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAA
 SEQ_LEN: 279
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 277
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: aaa`[[[_[NNNNNNTUP[[__`abbcccddddeeeeeeedddcdcccc``bbbbaaaba_`````bbbbba````____\\\\``_aabbbbbbbba````_WVV\\bbbb``\\`^_bXbbb_`_``bbbbbaaabbb___aabbaaa[[UUUbbbZZZZZabbbbbcaa[[UUU[[[[aabbbac____aPPNNNNPP]PPPWWabaaaabbbbbbbaaabbbbbaaabbbXXX__XXXXXXXXXXUYYUUUY[UUUYUUUUYXXMMMMRKMMMMM
+X_POS: 1426
+Y_POS: 1923
 ---
 SEQ_NAME: FQIBXOY01AV4UR
 SEQ: TCAGCTTGAGCAAATTCTTTATCTTTAAAATTAAACATTTTGTTGAAATTACTGTATCTTTAAAACTTAGATTCAATCGCTTCTTTTATTCTCTTCTGATGACACTCCTACTTGATTCGCAATAACTCAATCCAAACGACCAACCAATGTCAGCTAATTCATCAAGTTGTACGTCTAACGGCTTACCTGGTTTCTTCTTCCAGTTCTTGAACGTTTCCTAATGTGTTAAACCAACTTCTAAAGAAATTCAACCACATACGCAATCTTGCTATCTCGTAAATTTAAGTTG
 SEQ_LEN: 289
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 69
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: ```````````UUU\\`[[[]Wa]XXMMMMKKIIIRKMMMMRIIYY[[QQNSQ[[^^\]]][[XXRNNMXYZ\ZZZ[[XWXX[[[\[^JJRW\\WVVVV\\ZUUUUUUOOOMMMMVZSSRSSPPPPYXXXWVVWMMMSKMMMMMMMMMSVVVXXXSUOOOO\\UUUSOOOUUWWURSSUSMMMMMRRMMMUUMLIIRPTRRLLLLOOSRRRWWUUUOOMOOOSTTTTQQQKKIIKKKQKKKKKKMMKKKKKKKKKRUUUUUUVVVVVUTTUUURRPOKKKMMMKHKHHR
+X_POS: 248
+Y_POS: 3585
 ---
 SEQ_NAME: FQIBXOY01CU7IT
 SEQ: TCAGTTCGTAAAAGTGTGATAGATGATGGCAGATGTTATCTCTGTCCGTGTCTAGGCTATCCAAGACAATGGCGTTCAGAAGATATTTACCAGGAAATAAATGAGACGATACAAATAATAGAAATTTAAAATGCGCAAACCTGACCCAGTTTGCGCATTTTATGTTTTACACACGCGAGTAATGTGTTTACTTACGTGTGTTTATTTTGTTGCTGATTTTCAATTGTATATGAATGTGGTTGCACATAAATGCACTTTC
 SEQ_LEN: 259
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 257
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: eeeeeeeeeeeeeeeeeeeeeehhhghffgghhhhgghhhhhhhgffhheeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaaadeeeda]]]ddeeeeeeeeeeeeeeeeeedddedd]]]]dddeeeeeeeeeeeeeeeeedddeeedddddeeeeeeeeeeeeeeeeeeeeeedd\\\ddddeeeeeeeddddddddeeeeeeeeeeeedddddddedddddddddddaaadddddVVRY__]YPPMO
+X_POS: 1058
+Y_POS: 1859
 ---
 SEQ_NAME: FQIBXOY01CEZSI
 SEQ: TCAGAGGTTATGACGTTAAAGCTATTGATGGTCATTCGAACATAACAGAAGCAAGTTTGAAAAGTTCCAAAATATTTGTAATTCCTGAGGCTAACATTCCTTTCAAAGAATCAGAACAGGCAGCAATTGTTAAATATGTGAAACAAGGTGGCAATGTTGTCTTTATTTCAGATCATTACAATGCTGACCGAAATTTAAATCGTATTGATTCATCGGAGGCAATGAATGGTTATCGACGTGGAGCATATGAAGATATG
 SEQ_LEN: 257
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 253
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: eeeeeeeeeeeeeeeeedddddfhhfffffhfhhhhhhhhhhhhhhhhfeeeeeeddcccceeeeeeeeeeeeecccc```ddeeeedddddddeeddddeedd```eeeeeeeeeeeeeeeeeeeeeeeecccddeeee\\\deeeeeeeeeeeeeeeeeeeeeeeeeccceeeeeeeeeeeeeeeeed\\\ccceeeeeeeeeeeedddeeeeeeeeedddddddeefeddddddddddaaaddddd____^YYY
+X_POS: 873
+Y_POS: 3104
 ---
 SEQ_NAME: FQIBXOY01C4ETH
 SEQ: TCAGTGAAACAAACACGCAACAATCATTTGCTAATTGTAAGCAACTTAGACAAGTATATCCGAATGGTGTCACTGCCGATCATCCAGCATATCGACCACATTTAGATAGAGATAAAGATAAACGTGCATGTGAACCTGATAAATATTAAACAACAAGCGAATTGAATTCAAATTGTATTTAGCTTTATGCACTAATCACATAGTAAATAATGAGGGAGATTTTTTAGGCATGAGCAATCAATTCAAAAG
 SEQ_LEN: 249
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 248
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: eeeeeeeeeeeeeeeeeeeeeehgffaaahheggeddddddddegggfgeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeddddeeeeeeeeeeeeeeeeeedddeeedddddeeeeeeeeeeeeeeeeeeeeeeedd\\\adeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee`_____aaaddaaadddddd[[[[dZZZZ^
+X_POS: 1163
+Y_POS: 1139
 ---
 SEQ_NAME: FQIBXOY01BXD7A
 SEQ: TCAGAAAAGCTTTATAATTTTATAATTGCTAAATCTTTTCAACAACCAGTTGGAAGTACGTTCACTTATGGTGAATTAAGAAAGAAATATAATGTGGTTTGTAGCACGAATGATCAACGTGAAGTAGGACGTCGTTTTGCTTACTGGATTAAGTACACGCCAGGATTACCATTTAAAATGTAGGAACAAAAAATGGCAGTTATTATATCAGAAATAGGGATAAACCCATGTCAATAATAGCACGCCTTCGAAAGGAGGTGATTGCTAATGAGTTACACNTTAGTTTG
 SEQ_LEN: 287
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 177
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: ]]]XRRRR^^[[[^[^^^^^^[PTRWW```^^^WYW^^_^^]\XXVWWYXXWWXX\a\^^[[[\^^^^\]]\\XXXXVVXPPPVUWW]Z\\\^^^^^`^^WUW````^^^``__^^^^`^^[[[_\\\\\\\UPPPPPMVXXZXQUUVVVZZ^\XUUUUUUYZUOOMMMWWUUUMMMMJMMWRRMMMNNNNNNRRWURLLLRPPRTUUULLLLLRMUUURQOSSXTTMOOOWWWWWTTOQQQKKKQKKKKKKKKKKOKKKPKKKKPRROPKKKPRPOO@KKPPLKKK
+X_POS: 673
+Y_POS: 1172
 ---
 SEQ_NAME: FQIBXOY01BWE7M
 SEQ: TCAGTATGATGACGGCTAATGATGATGTAGAGGCGCCGAGTGACTTTGAAAAAATCAGAGCTGAAGTTTCATGGTAATAGATATTATCATTTTTGAATTAATTATATTAATGTGTTTAGCAATAGCACTGGAGGTGTTGTAAATATGTGGATTGTCATTTCAATTGTTTTATCTATATTTTTATTGATCTTGTTAAGTAGCATTTCTCATAAGATGAAAACCATAGAAGCATTGGAGTATATGAATG
 SEQ_LEN: 247
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 242
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: eeeeeeeeeeeeedddeeeeeehhhhhhhhhhhhhhhhhhhhhhhhff__ff__eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeedddeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaafddddaaadddddddeddddddddd
+X_POS: 662
+Y_POS: 880
 ---
 SEQ_NAME: FQIBXOY01A2RM8
 SEQ: TCAGAAACTAAAAAACTTAAAAAAGCATGCCAATCAGTACATCATAATTGCGTCTTGGGGACAGACAAATGATGAATAGAGATTGGCATGCTTTTTATTTTTGAATATAAATATTTAGTTCATGGCATTTCTAGTTACATGACGTCCATGAATTAAGAAGTAAACAAGCATAGTAATGATTGCTAAAGCGGCCATAAAGCCGAAGATTTCACTATATGAAAACATATGAGTAAATAACCCAAGGAATGATGGACCGAAGCCGAC
 SEQ_LEN: 264
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 261
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: ```^OOO[ULLLLLLS[[IIIIII[[`````bbbccddcccddddddddbbbbbbbbbbb__^_^[TTT__`bbbb`^_^bbbbbbbbb``YY^^Y`JJJJJZZZ]]XXZ``[TTTZ``]bbb`___ZZZ_]bb````^__b_^_^^`````bbbbbbbbb```b`````bbbb``]]]bb`]YSRRR`````]QQQR]]]`]]]]`b``XXX]`XXXXYYVVMVSZZZXSNNNNKKNNVXXSSSV][VPPPYYYYYYYYYYYY
+X_POS: 324
+Y_POS: 1762
 ---
 SEQ_NAME: FQIBXOY01API7E
 SEQ: TCAGCAATAGATATAATTTATGGTTTATATCTATTTCGGCATCTTTACCTTTCACTTGTTCAACTTATGTACCATAAATACTTCTGACAAGTTACTAATTAAACATGCAACCTCTAACTCAATTTAATATTTTAACTAACTTGTAATATACAGGATTCATCACGCATAATCAACCCTGTAAAACTTGATACGCAATAAAAGTTTTAAAGCATTTTATTGCGACAACTGTCTATCTATGTTTTTTCAAACGAATTTCATCAACTAGATTCCAGATAAATTC
 SEQ_LEN: 280
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 278
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: eeeeeeeeeeeeeeeeeeeeeeggfffffhffffffffffefeeeefeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeddddddeeeeeeeeeeeeeeeeedddeeeeeeeeee``\\\``eeddddeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeccccdddeeeeeedccccdeeeee```ceeee````WWceeeeeccccceedddddddddddddda\[[[^]]]adaaad_____________^^^_\\\\^___\\\\\\
+X_POS: 173
+Y_POS: 2792
 ---
 SEQ_NAME: FQIBXOY01BJJRF
 SEQ: TCAGTAACTATCAAATAAAATGATAACGGTTTCATCTATCTATTTTATCGGTCTAGTGGCTGATTTCAAGCTAGAAATATTGAATGACAATACAACTCTGTTAAAATGATGGACGTAGACAAATATGCGTATTGACGCTTTATTTTAAAAATTAACATGCTTATAACATGTTTATAGAAGGAGATTAACCTATGAACTATCAAGTTCTTTTATATTATAAATATATGACGATTGATGACCCTGAACAGTTTGCTCAGGATCAC
 SEQ_LEN: 263
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 260
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: cccc```ccbbb___bXXXXbbcccegeeddffffffedddecdddccccbbbccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccbbbccccccccbbbbccccccccccccccccccccccccccccccccccccccVVVVVVaccbbbcccccccccccccccccccccccccccccccccccaaaaccccccccccccaWRR\YVVVVVVYYYY
+X_POS: 515
+Y_POS: 2361
 ---

diff --git a/bp_test/out/read_sff.out.2 b/bp_test/out/read_sff.out.2
index 7591dc9c3162d08f1cd11fb59053af0cefcdd73a..7f9a466f92c9773211d9f1bf48e553fee63cf8a6 100644 (file)
--- a/bp_test/out/read_sff.out.2
+++ b/bp_test/out/read_sff.out.2
@@ -3,7 +3,9 @@ SEQ: TCAGTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAA
 SEQ_LEN: 279
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 277
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: aaa`[[[_[NNNNNNTUP[[__`abbcccddddeeeeeeedddcdcccc``bbbbaaaba_`````bbbbba````____\\\\``_aabbbbbbbba````_WVV\\bbbb``\\`^_bXbbb_`_``bbbbbaaabbb___aabbaaa[[UUUbbbZZZZZabbbbbcaa[[UUU[[[[aabbbac____aPPNNNNPP]PPPWWabaaaabbbbbbbaaabbbbbaaabbbXXX__XXXXXXXXXXUYYUUUY[UUUYUUUUYXXMMMMRKMMMMM
+X_POS: 1426
+Y_POS: 1923
 ---

diff --git a/bp_test/out/read_sff.out.3 b/bp_test/out/read_sff.out.3
index a8e3bcfebda07c3b758c68c537d3d749edfe13a3..b42ba33e674a6e36b2d3c9d48bf6aadd49de2d63 100644 (file)
--- a/bp_test/out/read_sff.out.3
+++ b/bp_test/out/read_sff.out.3
@@ -3,7 +3,9 @@ SEQ: tcagTCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAA
 SEQ_LEN: 279
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 277
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: aaa`[[[_[NNNNNNTUP[[__`abbcccddddeeeeeeedddcdcccc``bbbbaaaba_`````bbbbba````____\\\\``_aabbbbbbbba````_WVV\\bbbb``\\`^_bXbbb_`_``bbbbbaaabbb___aabbaaa[[UUUbbbZZZZZabbbbbcaa[[UUU[[[[aabbbac____aPPNNNNPP]PPPWWabaaaabbbbbbbaaabbbbbaaabbbXXX__XXXXXXXXXXUYYUUUY[UUUYUUUUYXXMMMMRKMMMMM
+X_POS: 1426
+Y_POS: 1923
 ---

diff --git a/bp_test/out/read_sff.out.4 b/bp_test/out/read_sff.out.4
index 9809971483e3efb36a588f1e40319e49b4bdfdc6..386e11ddcf6e897f2677ce389f7be59e47d88c92 100644 (file)
--- a/bp_test/out/read_sff.out.4
+++ b/bp_test/out/read_sff.out.4
@@ -3,7 +3,9 @@ SEQ: TCATATTTTTTAGAAACATGTTTGTTTGGACTCATTAATTCATGATTAAAATCACCATCATTCGTTATCAATAAA
 SEQ_LEN: 274
 CLIP_QUAL_LEFT: 4
 CLIP_QUAL_RIGHT: 277
-CLIP_ADAPTOR_LEFT: 0
-CLIP_ADAPTOR_RIGHT: 0
+CLIP_ADAPTOR_LEFT: -1
+CLIP_ADAPTOR_RIGHT: -1
 SCORES: [[[_[NNNNNNTUP[[__`abbcccddddeeeeeeedddcdcccc``bbbbaaaba_`````bbbbba````____\\\\``_aabbbbbbbba````_WVV\\bbbb``\\`^_bXbbb_`_``bbbbbaaabbb___aabbaaa[[UUUbbbZZZZZabbbbbcaa[[UUU[[[[aabbbac____aPPNNNNPP]PPPWWabaaaabbbbbbbaaabbbbbaaabbbXXX__XXXXXXXXXXUYYUUUY[UUUYUUUUYXXMMMMRKMMMM
+X_POS: 1426
+Y_POS: 1923
 ---