updated find_SNPs tests

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2104 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_test/in/find_SNPs.in b/bp_test/in/find_SNPs.in
index 5f4ffc8d827558bf5dd12da56c9f3cb2d58522f2..6402003565100c93d79457cff6c8e7e36e5ee71d 100644 (file)
--- a/bp_test/in/find_SNPs.in
+++ b/bp_test/in/find_SNPs.in
@@ -1,60 +1,117 @@
-MAPQ: 37
 STRAND: -
-Q_ID: ID00002249
-ALIGN: 63:->A
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450
+ALIGN: 156:T>G
 REC_TYPE: SAM
-S_BEG: 2937
-SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC
-CIGAR: 63M1I36M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6486413
+SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG
+CIGAR: 236M
+MD: 156T79
+S_END: 6486648
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00004198
-ALIGN: 8:G>C
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470
+ALIGN: 103:C>A
 REC_TYPE: SAM
-S_BEG: 993
-SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
-CIGAR: 100M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 306977
+SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA
+CIGAR: 233M
+MD: 103C129
+S_END: 307209
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00004198
-ALIGN: 8:G>C
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
+---
+STRAND: -
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
 REC_TYPE: SAM
-S_BEG: 993
-SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
-CIGAR: 100M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
 ---

diff --git a/bp_test/out/find_SNPs.out.1 b/bp_test/out/find_SNPs.out.1
index 2338ec0b8b1c1c843ca1b979e8b0d376e6ec2846..654152f11f9f17cd5f1e73818880e44111f6ae3d 100644 (file)
--- a/bp_test/out/find_SNPs.out.1
+++ b/bp_test/out/find_SNPs.out.1
@@ -1,81 +1,229 @@
-MAPQ: 37
 STRAND: -
-Q_ID: ID00002249
-ALIGN: 63:->A
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450
+ALIGN: 156:T>G
 REC_TYPE: SAM
-S_BEG: 2937
-SEQ: TCAACAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAAGTGCTGGGAGCGTTTTTGCCAGGAACTGGGTAAGC
-CIGAR: 63M1I36M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6486413
+SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG
+CIGAR: 236M
+MD: 156T79
+S_END: 6486648
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00004198
-ALIGN: 8:G>C
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470
+ALIGN: 103:C>A
 REC_TYPE: SAM
-S_BEG: 993
-SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
-CIGAR: 100M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 306977
+SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA
+CIGAR: 233M
+MD: 103C129
+S_END: 307209
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
+---
+STRAND: -
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00004198
-ALIGN: 8:G>C
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
 REC_TYPE: SAM
-S_BEG: 993
-SEQ: CGCCGATTCTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGTCAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAG
-CIGAR: 100M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
 ---
-MAPQ: 37
 STRAND: -
-Q_ID: ID00009237
-ALIGN: 61:G>-
-S_ID: gi|48994873|gb|U00096.2|
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
 REC_TYPE: SAM
-S_BEG: 5440
-SEQ: CCTACACGGACCGCCGCCACCGCCGCGCCACCATAAGAAAGCTCCTCATGATCATCACGGCGTCATGGTCCAGGCAAACATCACCGCTAAATGACAAATG
-CIGAR: 61M1D39M
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 6486569
+EVENT: T>G
+SNP_COUNT: 1
+TYPE: MISMATCH
 ---
 REC_TYPE: SNP
-S_ID: gi|48994873|gb|U00096.2|
-POS: 3000
-EVENT: ->A
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 307080
+EVENT: C>A
 SNP_COUNT: 1
-TYPE: INSERTION
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 6526270
+EVENT: T>A
+SNP_COUNT: 2
+TYPE: MISMATCH
 ---
 REC_TYPE: SNP
-S_ID: gi|48994873|gb|U00096.2|
-POS: 1001
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410279
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410287
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410313
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410317
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410322
 EVENT: G>C
 SNP_COUNT: 2
 TYPE: MISMATCH
 ---
 REC_TYPE: SNP
-S_ID: gi|48994873|gb|U00096.2|
-POS: 5501
-EVENT: G>-
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410348
+EVENT: T>A
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410353
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410368
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410369
+EVENT: G>T
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410373
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683519
+EVENT: C>G
 SNP_COUNT: 3
-TYPE: DELETION
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683538
+EVENT: T>G
+SNP_COUNT: 3
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683540
+EVENT: C>A
+SNP_COUNT: 3
+TYPE: MISMATCH
 ---

diff --git a/bp_test/out/find_SNPs.out.2 b/bp_test/out/find_SNPs.out.2
new file mode 100644 (file)
index 0000000..a98a084
--- /dev/null
+++ b/bp_test/out/find_SNPs.out.2
@@ -0,0 +1,245 @@
+STRAND: -
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14450:1450
+ALIGN: 156:T>G
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6486413
+SEQ: CTCGCCGGGCACTACCTGCGCTACGCCGGGCAGGCCGAATGGGAAAGCCTGCAGATCGAACCGGTGAAGGGCGGCTACCAGGCGAGCTTCGCCCTGATGCGCATCGGCAATCCGGAGAAACTGATGGAATATGGGCCCGCGGCGGTCGGCGAGTGGGCGGCTGGAGGGGCAAGGCGCCCTCTACCGACTGCGCAGCGAAGGCCTGGGCGCCGGCTGCAGCCTGCTGGTATGGCAGG
+CIGAR: 236M
+MD: 156T79
+S_END: 6486648
+---
+STRAND: -
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:14490:1470
+ALIGN: 103:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 306977
+SEQ: GCAAGGGATGGTGACCCGGTAGGCTGGGCCGGCCAGATCCACGGCGGTCCAGATACCGGCTATCACCCAGCCGACCGGCCCGGCTAGCGCGGCGACGGCACGAACGCCAGCGAAGGTTCCCCCAGCAACCACCGCACTGCGCAGCCCGTGCCCAAGCAGCTGCTGAGCCATCGAGTTCACGATCACCGTCGAAGTGCGATAGAGGATTAGCCGTGCTACGGTCGGCACTACCA
+CIGAR: 233M
+MD: 103C129
+S_END: 307209
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
+---
+STRAND: -
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
+---
+STRAND: -
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+STRAND: +
+MAPQ: 42
+NM: 1
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16598:1488
+ALIGN: 6:T>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 6526264
+SEQ: GCCAGCACCAGATCACGAGCCGCGCGGTTGGCAGCGTCCAGGCCGTCAGCGATCTTCTTCTGACGCTCTTGCAGAGCCGCGATGACCGGAGGCCACACGAACTTCATGCAGAACAGCACAAAGATGAAGAACGCAACGGACTGGCCAATCAGGGTTGCATTAATGTTCAC
+CIGAR: 170M
+MD: 6T163
+S_END: 6526433
+---
+STRAND: -
+MAPQ: 8
+NM: 10
+Q_ID: M01168:19:000000000-A2YGD:1:1101:15847:1490
+ALIGN: 54:C>G,62:C>G,88:C>G,92:T>G,97:G>C,123:T>A,128:C>G,143:T>G,144:G>T,148:T>G
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 1410225
+SEQ: GTCAGCGGCCGCCAGCGACGACAACGACGAGGAGCCCGCCGGGCAGGCGGGCGGGGAACAGGGCGAGGAGCGCCGCAGCCGGGTCCTGGGGGGCACCCCCGAGCGCCTGGACCGGCTGCTGGAAATCTGCAGCAAGTCGCTGGGTGAGGTCCAG
+CIGAR: 154M
+MD: 54C7C25C3T4G25T4C14T0G3T5
+S_END: 1410378
+---
+STRAND: -
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+STRAND: -
+MAPQ: 42
+NM: 3
+Q_ID: M01168:19:000000000-A2YGD:1:1101:16182:1497
+ALIGN: 201:C>G,220:T>G,222:C>A
+REC_TYPE: SAM
+S_ID: gi|116048575|ref|NC_008463.1|
+S_BEG: 2683318
+SEQ: TTGCAGCGCGCCTTGCGCTGACTGGCTCTTGCCGACCAGATCGGCCAGCACGCTTTCGTCTTCGCCCAGGTTCTGCGACACCTGCGCCTGCATCTGCATGGTGGTCTGCAAGCCGTTGAGCGTGTTCTTCCACCGCTCTTGGGCGTCGCGGTACATCTGGTCGCCGCTGACGGTGGCGGCGTACTGCTCCGGGTACAGGCGGGCGAACTCCCGATCCAGAGTAGTCACGTCGT
+CIGAR: 233M
+MD: 201C18T1C10
+S_END: 2683550
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 6486569
+COVERAGE: 1
+EVENT: T>G
+SNP_COUNT: 1
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 307080
+COVERAGE: 1
+EVENT: C>A
+SNP_COUNT: 1
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 6526270
+COVERAGE: 2
+EVENT: T>A
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410279
+COVERAGE: 2
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410287
+COVERAGE: 2
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410313
+COVERAGE: 2
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410317
+COVERAGE: 2
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410322
+COVERAGE: 2
+EVENT: G>C
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410348
+COVERAGE: 2
+EVENT: T>A
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410353
+COVERAGE: 2
+EVENT: C>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410368
+COVERAGE: 2
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410369
+COVERAGE: 2
+EVENT: G>T
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 1410373
+COVERAGE: 2
+EVENT: T>G
+SNP_COUNT: 2
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683519
+COVERAGE: 3
+EVENT: C>G
+SNP_COUNT: 3
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683538
+COVERAGE: 3
+EVENT: T>G
+SNP_COUNT: 3
+TYPE: MISMATCH
+---
+REC_TYPE: SNP
+S_ID: gi|116048575|ref|NC_008463.1|
+POS: 2683540
+COVERAGE: 3
+EVENT: C>A
+SNP_COUNT: 3
+TYPE: MISMATCH
+---