updated testing files for find_adaptor and clip_adaptor

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1907 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/clip_adaptor.in b/bp_test/in/clip_adaptor.in
index dd0bce5155a8e2031e63eb82f1c0f67c2e94b398..e8e5b8ebc5b958aebee20862f3b02e96ef84a8cd 100644 (file)
--- a/bp_test/in/clip_adaptor.in
+++ b/bp_test/in/clip_adaptor.in
@@ -1,8 +1,27 @@
-SEQ_NAME: 3_XeZ3OvwXsN1/1
-SEQ: CGCGAATCGGACTGGATNTCGCCGCTGACGACCTC
-SEQ_LEN: 35
-SCORES: a`_aa_^````\TY``WDGU[BBBBBBBBBBBBBB
-ADAPTOR_POS: 26
-ADAPTOR_LEN: 9
-ADAPTOR_MATCH: GACGACCTC
+SEQ_NAME: test
+SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG
+SEQ_LEN: 82
+SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 10
+ADAPTOR_PAT_LEFT: gatcgatcgt
+---
+SEQ_NAME: test
+SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG
+SEQ_LEN: 82
+SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh
+ADAPTOR_POS_RIGHT: 72
+ADAPTOR_LEN_RIGHT: 10
+ADAPTOR_PAT_RIGHT: tgctagctag
+---
+SEQ_NAME: test
+SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG
+SEQ_LEN: 82
+SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 10
+ADAPTOR_PAT_LEFT: gatcgatcgt
+ADAPTOR_POS_RIGHT: 72
+ADAPTOR_LEN_RIGHT: 10
+ADAPTOR_PAT_RIGHT: tgctagctag
 ---

diff --git a/bp_test/in/find_adaptor.in b/bp_test/in/find_adaptor.in
index 8bf5394295ae9414833824c8e45ea1c60c5c21f2..8454bfa3241764786ad94e71f3aa07b44f02cf0c 100644 (file)
--- a/bp_test/in/find_adaptor.in
+++ b/bp_test/in/find_adaptor.in
@@ -1,32 +1,88 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
 ---
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
 ---
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_full_length_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGA
+SEQ_LEN: 20
 ---
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_NAME: test_begin_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGAactacgt
 SEQ_LEN: 27
 ---
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
+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
+---
+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
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
 ---
-SEQ_NAME: test_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_mismatch
+SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt
+SEQ_LEN: 72
 ---
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_insertion
+SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt
+SEQ_LEN: 68
 ---
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_deletion
+SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt
+SEQ_LEN: 76
 ---

diff --git a/bp_test/out/clip_adaptor.out.1 b/bp_test/out/clip_adaptor.out.1
index 464527d6d5590e7568266d1b2c7a192bfbf33505..1a034570f8c6629ae2511d1e4b135ff88ba48eaf 100644 (file)
--- a/bp_test/out/clip_adaptor.out.1
+++ b/bp_test/out/clip_adaptor.out.1
@@ -1,8 +1,27 @@
-SEQ_NAME: 3_XeZ3OvwXsN1/1
-SEQ: CGCGAATCGGACTGGATNTCGCCGCT
-SEQ_LEN: 26
-SCORES: a`_aa_^````\TY``WDGU[BBBBB
-ADAPTOR_POS: 26
-ADAPTOR_LEN: 9
-ADAPTOR_MATCH: GACGACCTC
+SEQ_NAME: test
+SEQ: acgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagcaTGCTAGCTAG
+SEQ_LEN: 72
+SCORES: JKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDChhh
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 10
+ADAPTOR_PAT_LEFT: gatcgatcgt
+---
+SEQ_NAME: test
+SEQ: GATCGATCGTacgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagca
+SEQ_LEN: 72
+SCORES: @ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJ
+ADAPTOR_POS_RIGHT: 72
+ADAPTOR_LEN_RIGHT: 10
+ADAPTOR_PAT_RIGHT: tgctagctag
+---
+SEQ_NAME: test
+SEQ: acgagcagcatctgacgtatcgatcgttgattagttgctagctatgcagtctacgacgagca
+SEQ_LEN: 62
+SCORES: JKLMNOPQRSTUVWXYZ[\]^_`abcdefghhgfedcba`_^]\[ZYXWVUTSRQPONMLKJ
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 10
+ADAPTOR_PAT_LEFT: gatcgatcgt
+ADAPTOR_POS_RIGHT: 72
+ADAPTOR_LEN_RIGHT: 10
+ADAPTOR_PAT_RIGHT: tgctagctag
 ---

diff --git a/bp_test/out/find_adaptor.out.1 b/bp_test/out/find_adaptor.out.1
index f59114ee0809f628ffb48a6a12e615d92af46af4..eb723c99c3625d8e47f191bbea292b9d56faeb54 100644 (file)
--- a/bp_test/out/find_adaptor.out.1
+++ b/bp_test/out/find_adaptor.out.1
@@ -1,40 +1,106 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
----
-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
+---
+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
+---
+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
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
 ---
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
+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_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_mismatch
+SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt
+SEQ_LEN: 72
 ---
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_insertion
+SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt
+SEQ_LEN: 68
 ---
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
+SEQ_NAME: test_forward_and_reverse_match_with_deletion
+SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt
+SEQ_LEN: 76
 ---

diff --git a/bp_test/out/find_adaptor.out.10 b/bp_test/out/find_adaptor.out.10
new file mode 100644 (file)
index 0000000..f7f0b15
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.10
@@ -0,0 +1,130 @@
+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: 7
+ADAPTOR_LEN_LEFT: 22
+ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+ADAPTOR_POS_LEFT: 4
+ADAPTOR_LEN_LEFT: 22
+ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT
+---
+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
+---
+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
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 7
+ADAPTOR_LEN_RIGHT: 22
+ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 4
+ADAPTOR_LEN_RIGHT: 22
+ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT
+---
+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: 7
+ADAPTOR_LEN_LEFT: 22
+ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 43
+ADAPTOR_LEN_RIGHT: 22
+ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_RIGHT: 25
+ADAPTOR_LEN_RIGHT: 22
+ADAPTOR_PAT_RIGHT: gaTGACTACGACTACGACTACT
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+ADAPTOR_POS_LEFT: 7
+ADAPTOR_LEN_LEFT: 22
+ADAPTOR_PAT_LEFT: gaTCGTATGCCGTCTTCTGCTT
+---
+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
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 22
+ADAPTOR_PAT_LEFT: TCGTATGaaCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 47
+ADAPTOR_LEN_RIGHT: 22
+ADAPTOR_PAT_RIGHT: TGACTACGACTAaaCGACTACT
+---

diff --git a/bp_test/out/find_adaptor.out.2 b/bp_test/out/find_adaptor.out.2
index c5eb741e9b12a519f156c15e282c916293775ab8..3bfeedc71ed7f3a4a1e342ce5e84775142175560 100644 (file)
--- a/bp_test/out/find_adaptor.out.2
+++ b/bp_test/out/find_adaptor.out.2
@@ -1,42 +1,100 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+---
+SEQ_NAME: test_full_length_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGA
+SEQ_LEN: 20
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA
+---
+SEQ_NAME: test_begin_match_forward_rc
+SEQ: AAGCAGAAGACGGCATACGAactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA
+---
+SEQ_NAME: test_middle_match_forward_rc
+SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA
+---
+SEQ_NAME: test_end_match_forward_rc
+SEQ: gactgaAAGCAGAAGACGGCATACGA
+SEQ_LEN: 26
+ADAPTOR_POS_LEFT: 6
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: AAGCAGAAGACGGCATACGA
+---
+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
+---
+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
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
-ADAPTOR_POS: 28
-ADAPTOR_LEN: 5
----
-SEQ_NAME: test_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
+---
+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
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+---
+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
 ---

diff --git a/bp_test/out/find_adaptor.out.3 b/bp_test/out/find_adaptor.out.3
index 029538b5d743a8372699f7d2eb16dd8dc15ff332..1e7ac79d2d3b1614d22d383c564c66c1bfd5e2f3 100644 (file)
--- a/bp_test/out/find_adaptor.out.3
+++ b/bp_test/out/find_adaptor.out.3
@@ -1,42 +1,106 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+---
+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
+---
+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
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
----
-SEQ_NAME: test_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
+---
+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_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+---
+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
 ---

diff --git a/bp_test/out/find_adaptor.out.4 b/bp_test/out/find_adaptor.out.4
index 8da18a48462dcff23bed8c0a8b70d83197952d44..23667bb4b698c7aa0e1d5197996be80386337d17 100644 (file)
--- a/bp_test/out/find_adaptor.out.4
+++ b/bp_test/out/find_adaptor.out.4
@@ -1,42 +1,100 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_match
-SEQ: gactgaTCGTATGCCGTCTTCTGCTTG
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
+---
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+---
+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
+---
+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
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+---
+SEQ_NAME: test_full_length_match_reverse_rc
+SEQ: AGTAGTCGTAGTCGTAGTCA
+SEQ_LEN: 20
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA
+---
+SEQ_NAME: test_begin_match_reverse_rc
+SEQ: AGTAGTCGTAGTCGTAGTCAactacgt
 SEQ_LEN: 27
-ADAPTOR_POS: 6
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
----
-SEQ_NAME: test_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 19
----
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA
+---
+SEQ_NAME: test_middle_match_reverse_rc
+SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA
+---
+SEQ_NAME: test_end_match_reverse_rc
+SEQ: gactgaAGTAGTCGTAGTCGTAGTCA
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: AGTAGTCGTAGTCGTAGTCA
+---
+SEQ_NAME: test_forward_and_reverse_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 72
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+---
+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
 ---

diff --git a/bp_test/out/find_adaptor.out.5 b/bp_test/out/find_adaptor.out.5
index a337be4b10d91a831eebe31ca423e0aef093d773..c9f66db0b7d0d1ee4f9f82f8e7296ba2aa05a2c4 100644 (file)
--- a/bp_test/out/find_adaptor.out.5
+++ b/bp_test/out/find_adaptor.out.5
@@ -1,42 +1,124 @@
-SEQ_NAME: test_full_length_adaptor
-SEQ: TCGTATGCCGTCTTCTGCTTG
-SEQ_LEN: 21
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_begin_match
-SEQ: TCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 28
-ADAPTOR_POS: 0
-ADAPTOR_LEN: 21
----
-SEQ_NAME: test_middle_match
-SEQ: actgactgaTCGTATGCCGTCTTCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 7
-ADAPTOR_LEN: 23
----
-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
+---
+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
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
-ADAPTOR_POS: 4
-ADAPTOR_LEN: 23
----
-SEQ_NAME: test_end_trim
-SEQ: gtgacactatcgatacgatcgacactgaTCGTA
-SEQ_LEN: 33
----
-SEQ_NAME: test_mismatches
-SEQ: actgactgaTCGTATtCCGTCTTaTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_insertions
-SEQ: actgactgaTCGTATCCGTCTTTGCTTGactacgt
-SEQ_LEN: 37
----
-SEQ_NAME: test_deletions
-SEQ: actgactgaTCGTATgGCCGTCTTgCTGCTTGactacgt
-SEQ_LEN: 37
-ADAPTOR_POS: 9
-ADAPTOR_LEN: 23
+---
+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
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
 ---

diff --git a/bp_test/out/find_adaptor.out.6 b/bp_test/out/find_adaptor.out.6
new file mode 100644 (file)
index 0000000..5593ea1
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.6
@@ -0,0 +1,133 @@
+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
+---
+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
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 1
+ADAPTOR_PAT_LEFT: T
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 1
+ADAPTOR_PAT_LEFT: T
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 11
+ADAPTOR_PAT_LEFT: GTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+---

diff --git a/bp_test/out/find_adaptor.out.7 b/bp_test/out/find_adaptor.out.7
new file mode 100644 (file)
index 0000000..bbf6ebf
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.7
@@ -0,0 +1,169 @@
+SEQ_NAME: test_full_length_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 20
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 19
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: T
+---
+SEQ_NAME: test_begin_match_forward
+SEQ: TCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 26
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_middle_match_forward
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 35
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_end_match_forward
+SEQ: gactgaTCGTATGCCGTCTTCTGCTT
+SEQ_LEN: 26
+ADAPTOR_POS_LEFT: 6
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 25
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: T
+---
+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_RIGHT: 26
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_middle_match_forward_rc
+SEQ: actgactgaAAGCAGAAGACGGCATACGAactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 35
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_end_match_forward_rc
+SEQ: gactgaAAGCAGAAGACGGCATACGA
+SEQ_LEN: 26
+---
+SEQ_NAME: test_full_length_match_reverse
+SEQ: TGACTACGACTACGACTACT
+SEQ_LEN: 20
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 1
+ADAPTOR_PAT_LEFT: T
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 1
+ADAPTOR_PAT_LEFT: T
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_RIGHT: 26
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_middle_match_reverse_rc
+SEQ: actgactgaAGTAGTCGTAGTCGTAGTCAactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 35
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+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
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_LEFT: 0
+ADAPTOR_LEN_LEFT: 11
+ADAPTOR_PAT_LEFT: GTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_reverse_partial_match
+SEQ: actgactgaTCGTATGCCGTCTTCTGCTTactacgtactgactgaTGACTACGAC
+SEQ_LEN: 55
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTATGCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 10
+ADAPTOR_PAT_RIGHT: TGACTACGAC
+---
+SEQ_NAME: test_forward_and_reverse_match_with_mismatch
+SEQ: actgactgaTCGTAccCCGTCTTCTGCTTactacgtactgactgaTGACTACGAggACGACTACTactacgt
+SEQ_LEN: 72
+ADAPTOR_POS_RIGHT: 71
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_forward_and_reverse_match_with_insertion
+SEQ: actgactgaTCGTATCGTCTTCTGCTTactacgtactgactgaTGACTACGACCGACTACTactacgt
+SEQ_LEN: 68
+ADAPTOR_POS_RIGHT: 67
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---
+SEQ_NAME: test_forward_and_reverse_match_with_deletion
+SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt
+SEQ_LEN: 76
+ADAPTOR_POS_RIGHT: 75
+ADAPTOR_LEN_RIGHT: 1
+ADAPTOR_PAT_RIGHT: t
+---

diff --git a/bp_test/out/find_adaptor.out.8 b/bp_test/out/find_adaptor.out.8
new file mode 100644 (file)
index 0000000..1d7adab
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.8
@@ -0,0 +1,130 @@
+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
+---
+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
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 20
+ADAPTOR_PAT_LEFT: TCGTAccCCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGAggACGACTACT
+---
+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
+---

diff --git a/bp_test/out/find_adaptor.out.9 b/bp_test/out/find_adaptor.out.9
new file mode 100644 (file)
index 0000000..50442b8
--- /dev/null
+++ b/bp_test/out/find_adaptor.out.9
@@ -0,0 +1,130 @@
+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
+---
+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
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_begin_match_reverse
+SEQ: TGACTACGACTACGACTACTactacgt
+SEQ_LEN: 27
+ADAPTOR_POS_RIGHT: 0
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_middle_match_reverse
+SEQ: actgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 36
+ADAPTOR_POS_RIGHT: 9
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_end_match_reverse
+SEQ: gactgaTGACTACGACTACGACTACT
+SEQ_LEN: 26
+ADAPTOR_POS_RIGHT: 6
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_RIGHT: 45
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+SEQ_NAME: test_forward_partial_match
+SEQ: GTCTTCTGCTTactacgtactgactgaTGACTACGACTACGACTACTactacgt
+SEQ_LEN: 54
+ADAPTOR_POS_RIGHT: 27
+ADAPTOR_LEN_RIGHT: 20
+ADAPTOR_PAT_RIGHT: TGACTACGACTACGACTACT
+---
+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
+ADAPTOR_POS_LEFT: 9
+ADAPTOR_LEN_LEFT: 18
+ADAPTOR_PAT_LEFT: TCGTATCGTCTTCTGCTT
+ADAPTOR_POS_RIGHT: 43
+ADAPTOR_LEN_RIGHT: 18
+ADAPTOR_PAT_RIGHT: TGACTACGACCGACTACT
+---
+SEQ_NAME: test_forward_and_reverse_match_with_deletion
+SEQ: actgactgaTCGTATGaaCCGTCTTCTGCTTactacgtactgactgaTGACTACGACTAaaCGACTACTactacgt
+SEQ_LEN: 76
+---

diff --git a/bp_test/test/test_find_adaptor b/bp_test/test/test_find_adaptor
index cbbe4a79a2d08744b9dccc51e8d6d65af68cea7f..19f68fdad5e14815aee66db39378ae71cb835a53 100755 (executable)
--- a/bp_test/test/test_find_adaptor
+++ b/bp_test/test/test_find_adaptor
@@ -2,22 +2,42 @@
 
 source "$BP_DIR/bp_test/lib/test.sh"
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -I $in -O $tmp"
+run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -I $in -O $tmp"
 assert_no_diff $tmp $out.1
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 0 -p -l 5 -I $in -O $tmp"
+run "$bp -m 0 -i 0 -d 0 -F TCGTATGCCGTCTTCTGCTT -I $in -O $tmp"
 assert_no_diff $tmp $out.2
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 10 -i 0 -d 0 -I $in -O $tmp"
+run "$bp -m 0 -i 0 -d 0 -r TGACTACGACTACGACTACT -I $in -O $tmp"
 assert_no_diff $tmp $out.3
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 10 -d 0 -I $in -O $tmp"
+run "$bp -m 0 -i 0 -d 0 -R TGACTACGACTACGACTACT -I $in -O $tmp"
 assert_no_diff $tmp $out.4
 clean
 
-run "$bp -a TCGTATGCCGTCTTCTGCTTG -m 0 -i 0 -d 10 -I $in -O $tmp"
+run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp"
 assert_no_diff $tmp $out.5
 clean
+
+run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -I $in -O $tmp"
+assert_no_diff $tmp $out.6
+clean
+
+run "$bp -m 0 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -l 1 -r TGACTACGACTACGACTACT -L 1 -I $in -O $tmp"
+assert_no_diff $tmp $out.7
+clean
+
+run "$bp -m 10 -i 0 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp"
+assert_no_diff $tmp $out.8
+clean
+
+run "$bp -m 0 -i 10 -d 0 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp"
+assert_no_diff $tmp $out.9
+clean
+
+run "$bp -m 0 -i 0 -d 10 -f TCGTATGCCGTCTTCTGCTT -r TGACTACGACTACGACTACT -I $in -O $tmp"
+assert_no_diff $tmp $out.10
+clean