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gatk-3.8/public/testdata/exampleGRP.grp

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Extensive refactoring of the GATKReports. This was a beast. The practical differences between version 1.0 and this one (v1.1) are: * the underlying data structure now uses arrays instead of hashes, which should drastically reduce the memory overhead required to create large tables. * no more primary keys; you can still create arbitrary IDs to index into rows, but there is no special cased primary key column in the table. * no more dangerous/ugly table operations supported except to increment a cell's value (if an int) or to concatenate 2 tables. Integration tests change because table headers are different. Old classes are still lying around. Will clean those up in a subsequent commit.
2012-05-18 13:11:26 +08:00
#:GATKReport.v1.1:5
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
#:GATKTable:2:18:%s:%s:;
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
#:GATKTable:Arguments:Recalibration argument collection values used in this run
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
Argument Value
binary_tag_name null
covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate
default_platform null
deletions_default_quality 45
force_platform null
indels_context_size 3
insertions_default_quality 45
low_quality_tail 2
maximum_cycle_value 500
mismatches_context_size 2
mismatches_default_quality -1
no_standard_covs false
plot_pdf_file null
quantizing_levels 16
recalibration_report null
run_without_dbsnp false
solid_nocall_strategy THROW_EXCEPTION
solid_recal_mode SET_Q_ZERO
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
#:GATKTable:3:94:%s:%s:%s:;
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
#:GATKTable:Quantized:Quality quantization map
QualityScore Count QuantizedScore
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
0 0 8
1 0 8
2 0 8
3 0 8
4 0 8
5 0 8
6 11 8
7 0 8
8 7 8
9 4 8
10 1 8
11 2 8
12 4 19
13 3 19
14 1 19
15 5 19
16 10 19
17 6 19
18 7 19
19 15 19
20 5 19
21 17 19
22 9 19
23 15 23
24 20 24
25 15 13
26 6 13
27 22 27
28 15 28
29 20 29
30 20 30
31 25 31
32 32 32
33 35 33
34 36 34
35 0 93
36 0 93
37 0 93
38 0 93
39 0 93
40 0 93
41 0 93
42 0 93
43 0 93
44 0 93
45 736 45
46 0 93
47 0 93
48 0 93
49 0 93
50 0 93
51 0 93
52 0 93
53 0 93
54 0 93
55 0 93
56 0 93
57 0 93
58 0 93
59 0 93
60 0 93
61 0 93
62 0 93
63 0 93
64 0 93
65 0 93
66 0 93
67 0 93
68 0 93
69 0 93
70 0 93
71 0 93
72 0 93
73 0 93
74 0 93
75 0 93
76 0 93
77 0 93
78 0 93
79 0 93
80 0 93
81 0 93
82 0 93
83 0 93
84 0 93
85 0 93
86 0 93
87 0 93
88 0 93
89 0 93
90 0 93
91 0 93
92 0 93
93 0 93
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
#:GATKTable:6:3:%s:%s:%.4f:%.4f:%d:%.2f:;
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
#:GATKTable:RecalTable0:
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
ReadGroup EventType EmpiricalQuality EstimatedQReported Observations Errors
exampleBAM.bam M 17.0000 17.4959 368 11.00
exampleBAM.bam I 45.0000 45.0000 368 0.00
exampleBAM.bam D 45.0000 45.0000 368 0.00
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
#:GATKTable:6:30:%s:%s:%s:%.4f:%d:%.2f:;
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
#:GATKTable:RecalTable1:
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
ReadGroup QualityScore EventType EmpiricalQuality Observations Errors
exampleBAM.bam 6 M 6.0000 11 3.00
exampleBAM.bam 8 M 8.0000 7 1.00
exampleBAM.bam 9 M 9.0000 4 0.00
exampleBAM.bam 10 M 10.0000 1 0.00
exampleBAM.bam 11 M 11.0000 2 1.00
exampleBAM.bam 12 M 12.0000 4 0.00
exampleBAM.bam 13 M 13.0000 3 0.00
exampleBAM.bam 14 M 14.0000 1 0.00
exampleBAM.bam 15 M 15.0000 5 0.00
exampleBAM.bam 16 M 16.0000 10 1.00
exampleBAM.bam 17 M 17.0000 6 1.00
exampleBAM.bam 18 M 18.0000 7 1.00
exampleBAM.bam 19 M 19.0000 15 1.00
exampleBAM.bam 20 M 20.0000 5 1.00
exampleBAM.bam 21 M 21.0000 17 0.00
exampleBAM.bam 22 M 22.0000 9 0.00
exampleBAM.bam 23 M 23.0000 15 0.00
exampleBAM.bam 24 M 24.0000 20 1.00
exampleBAM.bam 25 M 25.0000 15 0.00
exampleBAM.bam 26 M 26.0000 6 0.00
exampleBAM.bam 27 M 27.0000 22 0.00
exampleBAM.bam 28 M 28.0000 15 0.00
exampleBAM.bam 29 M 29.0000 20 0.00
exampleBAM.bam 30 M 30.0000 20 0.00
exampleBAM.bam 31 M 31.0000 25 0.00
exampleBAM.bam 32 M 32.0000 32 0.00
exampleBAM.bam 33 M 33.0000 35 0.00
exampleBAM.bam 34 M 34.0000 36 0.00
exampleBAM.bam 45 I 45.0000 368 0.00
exampleBAM.bam 45 D 45.0000 368 0.00
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
#:GATKTable:8:952:%s:%s:%s:%s:%s:%.4f:%d:%.2f:;
BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00
#:GATKTable:RecalTable2:
Updating the exampleGRP.grp test file It had been generated with an old version of BQSRv2 and wasn't compatible with exampleBAM anymore.
2013-04-13 21:07:13 +08:00
ReadGroup QualityScore CovariateValue CovariateName EventType EmpiricalQuality Observations Errors
exampleBAM.bam 6 AA Context M 6.0000 1 0.00
exampleBAM.bam 6 GA Context M 6.0000 1 0.00
exampleBAM.bam 6 GC Context M 6.0000 2 2.00
exampleBAM.bam 6 TG Context M 6.0000 1 0.00
exampleBAM.bam 6 AT Context M 6.0000 1 0.00
exampleBAM.bam 6 CT Context M 6.0000 1 0.00
exampleBAM.bam 6 GT Context M 6.0000 2 0.00
exampleBAM.bam 6 TT Context M 6.0000 2 1.00
exampleBAM.bam 8 AA Context M 8.0000 1 0.00
exampleBAM.bam 8 GA Context M 8.0000 2 0.00
exampleBAM.bam 8 GC Context M 8.0000 1 0.00
exampleBAM.bam 8 TG Context M 8.0000 1 1.00
exampleBAM.bam 8 GT Context M 8.0000 2 0.00
exampleBAM.bam 9 TG Context M 9.0000 1 0.00
exampleBAM.bam 9 AT Context M 9.0000 1 0.00
exampleBAM.bam 9 CT Context M 9.0000 1 0.00
exampleBAM.bam 9 GT Context M 9.0000 1 0.00
exampleBAM.bam 10 TT Context M 10.0000 1 0.00
exampleBAM.bam 11 TC Context M 11.0000 1 1.00
exampleBAM.bam 11 GT Context M 11.0000 1 0.00
exampleBAM.bam 12 GA Context M 12.0000 1 0.00
exampleBAM.bam 12 CC Context M 12.0000 1 0.00
exampleBAM.bam 12 TC Context M 12.0000 1 0.00
exampleBAM.bam 12 AG Context M 12.0000 1 0.00
exampleBAM.bam 13 AA Context M 13.0000 1 0.00
exampleBAM.bam 13 AG Context M 13.0000 1 0.00
exampleBAM.bam 13 AT Context M 13.0000 1 0.00
exampleBAM.bam 14 GA Context M 14.0000 1 0.00
exampleBAM.bam 15 AA Context M 15.0000 2 0.00
exampleBAM.bam 15 GA Context M 15.0000 1 0.00
exampleBAM.bam 15 GT Context M 15.0000 2 0.00
exampleBAM.bam 16 AA Context M 16.0000 1 0.00
exampleBAM.bam 16 TA Context M 16.0000 4 1.00
exampleBAM.bam 16 TC Context M 16.0000 1 0.00
exampleBAM.bam 16 GG Context M 16.0000 1 0.00
exampleBAM.bam 16 TG Context M 16.0000 1 0.00
exampleBAM.bam 16 CT Context M 16.0000 1 0.00
exampleBAM.bam 16 GT Context M 16.0000 1 0.00
exampleBAM.bam 17 CA Context M 17.0000 1 0.00
exampleBAM.bam 17 TA Context M 17.0000 1 0.00
exampleBAM.bam 17 TG Context M 17.0000 1 1.00
exampleBAM.bam 17 GT Context M 17.0000 1 0.00
exampleBAM.bam 17 TT Context M 17.0000 2 0.00
exampleBAM.bam 18 AC Context M 18.0000 1 0.00
exampleBAM.bam 18 TC Context M 18.0000 1 1.00
exampleBAM.bam 18 AT Context M 18.0000 1 0.00
exampleBAM.bam 18 GT Context M 18.0000 1 0.00
exampleBAM.bam 18 TT Context M 18.0000 2 0.00
exampleBAM.bam 19 AA Context M 19.0000 2 0.00
exampleBAM.bam 19 CA Context M 19.0000 2 0.00
exampleBAM.bam 19 GA Context M 19.0000 2 0.00
exampleBAM.bam 19 TA Context M 19.0000 3 0.00
exampleBAM.bam 19 GC Context M 19.0000 1 0.00
exampleBAM.bam 19 GG Context M 19.0000 1 0.00
exampleBAM.bam 19 TG Context M 19.0000 2 1.00
exampleBAM.bam 19 GT Context M 19.0000 1 0.00
exampleBAM.bam 19 TT Context M 19.0000 1 0.00
exampleBAM.bam 20 AA Context M 20.0000 1 0.00
exampleBAM.bam 20 CA Context M 20.0000 1 0.00
exampleBAM.bam 20 CC Context M 20.0000 1 0.00
exampleBAM.bam 20 TG Context M 20.0000 1 0.00
exampleBAM.bam 20 TT Context M 20.0000 1 1.00
exampleBAM.bam 21 CA Context M 21.0000 1 0.00
exampleBAM.bam 21 GA Context M 21.0000 1 0.00
exampleBAM.bam 21 TA Context M 21.0000 1 0.00
exampleBAM.bam 21 CC Context M 21.0000 1 0.00
exampleBAM.bam 21 TC Context M 21.0000 2 0.00
exampleBAM.bam 21 AG Context M 21.0000 1 0.00
exampleBAM.bam 21 GG Context M 21.0000 4 0.00
exampleBAM.bam 21 TG Context M 21.0000 1 0.00
exampleBAM.bam 21 AT Context M 21.0000 2 0.00
exampleBAM.bam 21 CT Context M 21.0000 1 0.00
exampleBAM.bam 21 GT Context M 21.0000 2 0.00
exampleBAM.bam 22 CA Context M 22.0000 1 0.00
exampleBAM.bam 22 GA Context M 22.0000 3 0.00
exampleBAM.bam 22 TA Context M 22.0000 1 0.00
exampleBAM.bam 22 GC Context M 22.0000 1 0.00
exampleBAM.bam 22 GG Context M 22.0000 1 0.00
exampleBAM.bam 22 TG Context M 22.0000 1 0.00
exampleBAM.bam 22 TT Context M 22.0000 1 0.00
exampleBAM.bam 23 AA Context M 23.0000 1 0.00
exampleBAM.bam 23 CA Context M 23.0000 1 0.00
exampleBAM.bam 23 TA Context M 23.0000 1 0.00
exampleBAM.bam 23 CC Context M 23.0000 2 0.00
exampleBAM.bam 23 GC Context M 23.0000 1 0.00
exampleBAM.bam 23 TC Context M 23.0000 2 0.00
exampleBAM.bam 23 GG Context M 23.0000 1 0.00
exampleBAM.bam 23 TG Context M 23.0000 3 0.00
exampleBAM.bam 23 AT Context M 23.0000 1 0.00
exampleBAM.bam 23 TT Context M 23.0000 2 0.00
exampleBAM.bam 24 CA Context M 24.0000 3 0.00
exampleBAM.bam 24 GA Context M 24.0000 2 0.00
exampleBAM.bam 24 TA Context M 24.0000 2 1.00
exampleBAM.bam 24 GC Context M 24.0000 1 0.00
exampleBAM.bam 24 AG Context M 24.0000 2 0.00
exampleBAM.bam 24 CG Context M 24.0000 1 0.00
exampleBAM.bam 24 GG Context M 24.0000 3 0.00
exampleBAM.bam 24 AT Context M 24.0000 1 0.00
exampleBAM.bam 24 CT Context M 24.0000 1 0.00
exampleBAM.bam 24 GT Context M 24.0000 1 0.00
exampleBAM.bam 24 TT Context M 24.0000 3 0.00
exampleBAM.bam 25 AA Context M 25.0000 2 0.00
exampleBAM.bam 25 CA Context M 25.0000 1 0.00
exampleBAM.bam 25 GG Context M 25.0000 2 0.00
exampleBAM.bam 25 TG Context M 25.0000 2 0.00
exampleBAM.bam 25 AT Context M 25.0000 2 0.00
exampleBAM.bam 25 GT Context M 25.0000 1 0.00
exampleBAM.bam 25 TT Context M 25.0000 5 0.00
exampleBAM.bam 26 TA Context M 26.0000 1 0.00
exampleBAM.bam 26 GG Context M 26.0000 1 0.00
exampleBAM.bam 26 TG Context M 26.0000 1 0.00
exampleBAM.bam 26 AT Context M 26.0000 1 0.00
exampleBAM.bam 26 GT Context M 26.0000 1 0.00
exampleBAM.bam 26 TT Context M 26.0000 1 0.00
exampleBAM.bam 27 AA Context M 27.0000 2 0.00
exampleBAM.bam 27 CA Context M 27.0000 1 0.00
exampleBAM.bam 27 TA Context M 27.0000 1 0.00
exampleBAM.bam 27 TC Context M 27.0000 2 0.00
exampleBAM.bam 27 AG Context M 27.0000 3 0.00
exampleBAM.bam 27 GG Context M 27.0000 3 0.00
exampleBAM.bam 27 TG Context M 27.0000 2 0.00
exampleBAM.bam 27 AT Context M 27.0000 4 0.00
exampleBAM.bam 27 CT Context M 27.0000 2 0.00
exampleBAM.bam 27 TT Context M 27.0000 2 0.00
exampleBAM.bam 28 AA Context M 28.0000 1 0.00
exampleBAM.bam 28 CA Context M 28.0000 1 0.00
exampleBAM.bam 28 TA Context M 28.0000 2 0.00
exampleBAM.bam 28 AG Context M 28.0000 3 0.00
exampleBAM.bam 28 GG Context M 28.0000 3 0.00
exampleBAM.bam 28 TG Context M 28.0000 1 0.00
exampleBAM.bam 28 GT Context M 28.0000 4 0.00
exampleBAM.bam 29 CA Context M 29.0000 1 0.00
exampleBAM.bam 29 TA Context M 29.0000 1 0.00
exampleBAM.bam 29 AC Context M 29.0000 1 0.00
exampleBAM.bam 29 CC Context M 29.0000 1 0.00
exampleBAM.bam 29 GC Context M 29.0000 1 0.00
exampleBAM.bam 29 AG Context M 29.0000 3 0.00
exampleBAM.bam 29 CG Context M 29.0000 1 0.00
exampleBAM.bam 29 GG Context M 29.0000 4 0.00
exampleBAM.bam 29 TG Context M 29.0000 1 0.00
exampleBAM.bam 29 AT Context M 29.0000 1 0.00
exampleBAM.bam 29 GT Context M 29.0000 1 0.00
exampleBAM.bam 29 TT Context M 29.0000 4 0.00
exampleBAM.bam 30 AA Context M 30.0000 2 0.00
exampleBAM.bam 30 CA Context M 30.0000 1 0.00
exampleBAM.bam 30 AC Context M 30.0000 4 0.00
exampleBAM.bam 30 CC Context M 30.0000 1 0.00
exampleBAM.bam 30 TC Context M 30.0000 2 0.00
exampleBAM.bam 30 AG Context M 30.0000 3 0.00
exampleBAM.bam 30 GG Context M 30.0000 1 0.00
exampleBAM.bam 30 TG Context M 30.0000 1 0.00
exampleBAM.bam 30 AT Context M 30.0000 2 0.00
exampleBAM.bam 30 CT Context M 30.0000 2 0.00
exampleBAM.bam 30 GT Context M 30.0000 1 0.00
exampleBAM.bam 31 CA Context M 31.0000 1 0.00
exampleBAM.bam 31 GA Context M 31.0000 1 0.00
exampleBAM.bam 31 CC Context M 31.0000 2 0.00
exampleBAM.bam 31 GC Context M 31.0000 2 0.00
exampleBAM.bam 31 AG Context M 31.0000 2 0.00
exampleBAM.bam 31 GG Context M 31.0000 6 0.00
exampleBAM.bam 31 TG Context M 31.0000 2 0.00
exampleBAM.bam 31 AT Context M 31.0000 2 0.00
exampleBAM.bam 31 CT Context M 31.0000 2 0.00
exampleBAM.bam 31 GT Context M 31.0000 1 0.00
exampleBAM.bam 31 TT Context M 31.0000 3 0.00
exampleBAM.bam 32 CA Context M 32.0000 2 0.00
exampleBAM.bam 32 TA Context M 32.0000 1 0.00
exampleBAM.bam 32 AC Context M 32.0000 1 0.00
exampleBAM.bam 32 CC Context M 32.0000 1 0.00
exampleBAM.bam 32 TC Context M 32.0000 1 0.00
exampleBAM.bam 32 AG Context M 32.0000 1 0.00
exampleBAM.bam 32 CG Context M 32.0000 1 0.00
exampleBAM.bam 32 GG Context M 32.0000 8 0.00
exampleBAM.bam 32 TG Context M 32.0000 3 0.00
exampleBAM.bam 32 AT Context M 32.0000 4 0.00
exampleBAM.bam 32 CT Context M 32.0000 2 0.00
exampleBAM.bam 32 TT Context M 32.0000 6 0.00
exampleBAM.bam 33 CA Context M 33.0000 2 0.00
exampleBAM.bam 33 GA Context M 33.0000 2 0.00
exampleBAM.bam 33 TA Context M 33.0000 1 0.00
exampleBAM.bam 33 AC Context M 33.0000 1 0.00
exampleBAM.bam 33 CC Context M 33.0000 2 0.00
exampleBAM.bam 33 GC Context M 33.0000 1 0.00
exampleBAM.bam 33 TC Context M 33.0000 3 0.00
exampleBAM.bam 33 AG Context M 33.0000 2 0.00
exampleBAM.bam 33 CG Context M 33.0000 1 0.00
exampleBAM.bam 33 GG Context M 33.0000 2 0.00
exampleBAM.bam 33 TG Context M 33.0000 5 0.00
exampleBAM.bam 33 AT Context M 33.0000 2 0.00
exampleBAM.bam 33 CT Context M 33.0000 4 0.00
exampleBAM.bam 33 GT Context M 33.0000 1 0.00
exampleBAM.bam 33 TT Context M 33.0000 4 0.00
exampleBAM.bam 34 AA Context M 34.0000 1 0.00
exampleBAM.bam 34 CA Context M 34.0000 3 0.00
exampleBAM.bam 34 GA Context M 34.0000 1 0.00
exampleBAM.bam 34 TA Context M 34.0000 2 0.00
exampleBAM.bam 34 AC Context M 34.0000 1 0.00
exampleBAM.bam 34 CC Context M 34.0000 1 0.00
exampleBAM.bam 34 GC Context M 34.0000 2 0.00
exampleBAM.bam 34 TC Context M 34.0000 6 0.00
exampleBAM.bam 34 AG Context M 34.0000 1 0.00
exampleBAM.bam 34 CG Context M 34.0000 1 0.00
exampleBAM.bam 34 GG Context M 34.0000 1 0.00
exampleBAM.bam 34 TG Context M 34.0000 4 0.00
exampleBAM.bam 34 AT Context M 34.0000 4 0.00
exampleBAM.bam 34 CT Context M 34.0000 2 0.00
exampleBAM.bam 34 GT Context M 34.0000 1 0.00
exampleBAM.bam 34 TT Context M 34.0000 5 0.00
exampleBAM.bam 45 AAA Context I 45.0000 5 0.00
exampleBAM.bam 45 AAA Context D 45.0000 5 0.00
exampleBAM.bam 45 CAA Context I 45.0000 5 0.00
exampleBAM.bam 45 CAA Context D 45.0000 5 0.00
exampleBAM.bam 45 GAA Context I 45.0000 2 0.00
exampleBAM.bam 45 GAA Context D 45.0000 2 0.00
exampleBAM.bam 45 TAA Context I 45.0000 6 0.00
exampleBAM.bam 45 TAA Context D 45.0000 6 0.00
exampleBAM.bam 45 ACA Context I 45.0000 4 0.00
exampleBAM.bam 45 ACA Context D 45.0000 4 0.00
exampleBAM.bam 45 CCA Context I 45.0000 8 0.00
exampleBAM.bam 45 CCA Context D 45.0000 8 0.00
exampleBAM.bam 45 GCA Context I 45.0000 5 0.00
exampleBAM.bam 45 GCA Context D 45.0000 5 0.00
exampleBAM.bam 45 TCA Context I 45.0000 6 0.00
exampleBAM.bam 45 TCA Context D 45.0000 6 0.00
exampleBAM.bam 45 AGA Context I 45.0000 5 0.00
exampleBAM.bam 45 AGA Context D 45.0000 5 0.00
exampleBAM.bam 45 GGA Context I 45.0000 3 0.00
exampleBAM.bam 45 GGA Context D 45.0000 3 0.00
exampleBAM.bam 45 TGA Context I 45.0000 10 0.00
exampleBAM.bam 45 TGA Context D 45.0000 10 0.00
exampleBAM.bam 45 ATA Context I 45.0000 6 0.00
exampleBAM.bam 45 ATA Context D 45.0000 6 0.00
exampleBAM.bam 45 CTA Context I 45.0000 3 0.00
exampleBAM.bam 45 CTA Context D 45.0000 3 0.00
exampleBAM.bam 45 GTA Context I 45.0000 2 0.00
exampleBAM.bam 45 GTA Context D 45.0000 2 0.00
exampleBAM.bam 45 TTA Context I 45.0000 11 0.00
exampleBAM.bam 45 TTA Context D 45.0000 11 0.00
exampleBAM.bam 45 CAC Context I 45.0000 6 0.00
exampleBAM.bam 45 CAC Context D 45.0000 6 0.00
exampleBAM.bam 45 GAC Context I 45.0000 2 0.00
exampleBAM.bam 45 GAC Context D 45.0000 2 0.00
exampleBAM.bam 45 TAC Context I 45.0000 1 0.00
exampleBAM.bam 45 TAC Context D 45.0000 1 0.00
exampleBAM.bam 45 ACC Context I 45.0000 3 0.00
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exampleBAM.bam 45 CCC Context I 45.0000 1 0.00
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BQSR Gatherer implementation and integration tests * restructured the hash tables into one class (RecalibrationReport) that has all the functionality for the different tables and key managers * optmized empirical qual calculation when merging recalibration reports * centralized the quality score quantization functionalities * unified the creating/loading of all the key manager/hash table structures. * added unit tests for the gatherer (disabled because gatk report needs to be sorted for automated testing) * added integration tests for BQSR and on-the-fly recalibration
2012-03-24 05:17:32 +08:00