Mercurial > repos > blankenberg > naive_variant_caller

annotate test-data/phiX174.fasta @ 3:90c9eb133c86

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More integer checking fixes.
author Daniel Blankenberg <dan@bx.psu.edu>
date Mon, 16 Sep 2013 10:16:02 -0400
parents ae6edc0012ba
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
1 >phiX174
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
2 GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
3 GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
4 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
5 TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
6 GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
7 TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
8 TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
9 CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
10 TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
11 TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
12 GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
13 CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
14 TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
15 AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
16 CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
17 TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
18 TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
19 CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
20 GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
21 GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
22 ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
23 TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
24 TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
25 ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
26 CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
27 GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
28 CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
29 TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
30 TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
31 TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
32 AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
33 TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
34 ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
35 GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
36 TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
37 TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
38 TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
39 TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
40 CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
41 AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
42 CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
43 TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
44 CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
45 AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
46 GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
47 GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
48 TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
49 CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
50 TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
51 GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
52 CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
53 TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
54 AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
55 TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
56 CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
57 TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
58 TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
59 CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
60 TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
61 ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
62 TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
63 ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
64 GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
65 CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
66 GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
67 GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
68 ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
69 CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
70 CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
71 GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
72 CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
73 CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
74 TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
75 TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
76 TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
77 AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
78 TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
ae6edc0012ba Populate naive_variant_caller repository.
Daniel Blankenberg <dan@bx.psu.edu>
parents:
diff changeset
79