refactoring of assemble_pairs

[biopieces.git] / bp_test / out / find_adaptor.out.1

diff --git a/bp_test/out/find_adaptor.out.1 b/bp_test/out/find_adaptor.out.1
index a177def7c1a1038e3c346dff8faab999cb8ddaf6..eb723c99c3625d8e47f191bbea292b9d56faeb54 100644 (file)
--- a/bp_test/out/find_adaptor.out.1
+++ b/bp_test/out/find_adaptor.out.1
@@ -1,56 +1,106 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+ADAPTOR_POS_LEFT: 6
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_full_length_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGA
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGAactacgt
 SEQ_LEN: 27
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_pos_begin
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTGgactgaTCGTATGCCGTCTTCTGCTTGacgta
-SEQ_LEN: 59
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
-ADAPTOR_MATCH: TCGTATGCCGTCTTCTGCTTG
----
-SEQ_NAME: test_edit_dist_5
-SEQ: actgactgaTCGGATGCGGTCTCATGTTGactacgt
+---
+SEQ_NAME: test_middle_match_forward_rc
+SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_forward_rc
+SEQ: gactgaAAGCAGAAGACGGCATACGA
+SEQ_LEN: 26
+---
+SEQ_NAME: test_full_length_match_reverse
+SEQ: TGACTACGACTACGACTACT
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
 SEQ_LEN: 36
-ADAPTOR_POS: 32
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: acgt
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
-ADAPTOR_MATCH: TCGTA
----
-SEQ_NAME: test_end_trim_edit_dist_1
-SEQ: gatgatcgtagcgatcgatcgacgctgaTCGTG
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 4
-ADAPTOR_MATCH: TCGT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+---
+SEQ_NAME: test_full_length_match_reverse_rc
+SEQ: AGTAGTCGTAGTCGTAGTCA
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_reverse_rc
+SEQ: AGTAGTCGTAGTCGTAGTCAactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_reverse_rc
+SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_reverse_rc
+SEQ: gactgaAGTAGTCGTAGTCGTAGTCA
+SEQ_LEN: 26
+---
+SEQ_NAME: test_forward_and_reverse_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 72
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_forward_and_reverse_match_with_mismatch
+SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt
+SEQ_LEN: 72
+---
+SEQ_NAME: test_forward_and_reverse_match_with_insertion
+SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt
+SEQ_LEN: 68
+---
+SEQ_NAME: test_forward_and_reverse_match_with_deletion
+SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt
+SEQ_LEN: 76
 ---