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Merge branch 'release/0.04'

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2 parents ec0be10 + 650b661 commit 0e506d7b59417bf3c6ef2c2c6640870acb1496d0 @sb10 sb10 committed Jul 11, 2012
Showing with 10,837 additions and 1,997 deletions.
  1. +2 −1 Build.PL
  2. +3 −1 HISTORY
  3. +1,318 −0 modules/Bio/Tools/NonStandardGFF.pm
  4. +34 −6 modules/LSF.pm
  5. +94 −0 modules/Pathogens/Import/CompressAndValidate.pm
  6. +70 −0 modules/Pathogens/Import/ValidateFastqConversion.pm
  7. +146 −0 modules/Pathogens/RNASeq/AlignmentSlice.pm
  8. +47 −0 modules/Pathogens/RNASeq/BAMStats.pm
  9. +113 −0 modules/Pathogens/RNASeq/BitWise.pm
  10. +165 −0 modules/Pathogens/RNASeq/CoveragePlot.pm
  11. +12 −0 modules/Pathogens/RNASeq/Exceptions.pm
  12. +180 −0 modules/Pathogens/RNASeq/Expression.pm
  13. +103 −0 modules/Pathogens/RNASeq/ExpressionStatsSpreadsheet.pm
  14. +103 −0 modules/Pathogens/RNASeq/Feature.pm
  15. +68 −0 modules/Pathogens/RNASeq/FeaturesTabFile.pm
  16. +85 −0 modules/Pathogens/RNASeq/GFF.pm
  17. +47 −0 modules/Pathogens/RNASeq/IntergenicFeature.pm
  18. +113 −0 modules/Pathogens/RNASeq/IntergenicRegions.pm
  19. +142 −0 modules/Pathogens/RNASeq/Read.pm
  20. +19 −0 modules/Pathogens/RNASeq/SequenceFile.pm
  21. +12 −0 modules/Pathogens/RNASeq/StandardProtocol/AlignmentSlice.pm
  22. +38 −0 modules/Pathogens/RNASeq/StandardProtocol/Read.pm
  23. +12 −0 modules/Pathogens/RNASeq/StrandSpecificProtocol/AlignmentSlice.pm
  24. +49 −0 modules/Pathogens/RNASeq/StrandSpecificProtocol/Read.pm
  25. +100 −0 modules/Pathogens/RNASeq/ValidateInputs.pm
  26. +82 −0 modules/Pathogens/Reports/Mapping/Report.pm
  27. +403 −0 modules/Pathogens/Reports/Mapping/Row.pm
  28. +77 −0 modules/Pathogens/Reports/Mapping/Spreadsheet.pm
  29. +125 −0 modules/VRTrack/AutoQC.pm
  30. +6 −2 modules/VRTrack/Core_obj.pm
  31. +2 −4 modules/VRTrack/Factory.pm
  32. +30 −0 modules/VRTrack/Lane.pm
  33. +114 −1 modules/VRTrack/Mapstats.pm
  34. +81 −23 modules/VRTrack/VRTrack.pm
  35. +53 −3 modules/Vcf.pm
  36. +868 −0 modules/VertRes/Pipelines/Assembly.pm
  37. +28 −0 modules/VertRes/Pipelines/Import.pm
  38. +154 −44 modules/VertRes/Pipelines/Import_iRODS_fastq.pm
  39. +118 −18 modules/VertRes/Pipelines/Mapping.pm
  40. +366 −0 modules/VertRes/Pipelines/RNASeqExpression.pm
  41. +16 −6 modules/VertRes/Pipelines/TrackQC_Bam.pm
  42. +25 −13 modules/VertRes/Pipelines/TrackQC_Fastq.pm
  43. 0 {web_code/qc_grind → modules/VertRes/QCGrind}/Util.pm
  44. +316 −0 modules/VertRes/QCGrind/ViewUtil.pm
  45. +292 −0 modules/VertRes/Utils/Assemblers/velvet.pm
  46. +140 −0 modules/VertRes/Utils/Assembly.pm
  47. +8 −3 modules/VertRes/Utils/Mappers/smalt.pm
  48. +204 −0 modules/VertRes/Utils/Mappers/tophat.pm
  49. +20 −1 modules/VertRes/Utils/Mapping.pm
  50. +50 −1 modules/VertRes/Utils/Sam.pm
  51. +68 −0 modules/VertRes/Utils/Scaffold.pm
  52. +115 −0 modules/VertRes/Utils/Scaffolders/sspace.pm
  53. +16 −0 modules/VertRes/Wrapper/WrapperI.pm
  54. +1 −1 modules/VertRes/Wrapper/bowtie.pm
  55. +6 −0 modules/VertRes/Wrapper/picard.pm
  56. +5 −0 modules/VertRes/Wrapper/samtools.pm
  57. +42 −25 modules/VertRes/Wrapper/smalt.pm
  58. +337 −0 modules/VertRes/Wrapper/tophat.pm
  59. BIN scripts/bamcheck
  60. +6 −1 scripts/bamcheck-mousewrapper
  61. +55 −13 scripts/bamcheck.c
  62. +790 −0 scripts/plot-bamcheck-2012-02-11
  63. +82 −0 scripts/rna_seq_expression
  64. +9 −1 scripts/run-beagle
  65. +4 −4 scripts/run-mpileup
  66. +96 −6 scripts/run-pipeline
  67. +27 −0 scripts/tweak-lane
  68. +13 −6 scripts/update_db_vrpipe.sh
  69. +1 −1 scripts/vcf-annotate
  70. +198 −0 scripts/vcf-contrast
  71. +8 −2 scripts/vcf-fix-ploidy
  72. +7 −2 scripts/vcf-isec
  73. +25 −3 scripts/vr-wrapper
  74. +13 −3 scripts/vrtrack_npg_gt_update
  75. +16 −22 scripts/vrtracking_tool
  76. +23 −3 scripts/weekly_new_lane_report
  77. +2 −0 sql/VRTrack_schema_17_to_18.sql
  78. +7 −0 sql/VRTrack_schema_18_to_19.sql
  79. +16 −0 sql/VRTrack_schema_19_to_20.sql
  80. +49 −0 t/Pathogens/AlignmentSlice.t
  81. +51 −0 t/Pathogens/BitWise.t
  82. +144 −0 t/Pathogens/CompressAndValidate.t
  83. +62 −0 t/Pathogens/CoveragePlot.t
  84. +82 −0 t/Pathogens/ExpressionStatsSpreadsheet.t
  85. +55 −0 t/Pathogens/FeaturesTabFile.t
  86. +36 −0 t/Pathogens/GFF.t
  87. +22 −0 t/Pathogens/IntergenicFeature.t
  88. +51 −0 t/Pathogens/IntergenicRegions.t
  89. +23 −0 t/Pathogens/MappingBamcheckGraphs.t
  90. +273 −0 t/Pathogens/MappingReport.t
  91. +63 −0 t/Pathogens/QCMappings.t
  92. +51 −0 t/Pathogens/Read.t
  93. +13 −0 t/Pathogens/SequenceFile.t
  94. +26 −0 t/Pathogens/StrandSpecificProtocolRead.t
  95. +40 −0 t/Pathogens/ValidateFastqConversion.t
  96. +29 −0 t/Pathogens/ValidateInputs.t
  97. +66 −0 t/Pathogens/VertResUtilsSam.t
  98. +30 −1 t/VRTrack/hierarchy_noreq.t
  99. +29 −1 t/VRTrack/non_core_classes.t
  100. +95 −0 t/VertRes/Wrapper/tophat.t
  101. +84 −0 t/data/1kg_lane_sq_invalid.gff
  102. +84 −0 t/data/1kg_lane_sq_valid.gff
  103. +24 −0 t/data/Citrobacter_rodentium_ICC168_v1_test.gff
  104. +27 −0 t/data/Citrobacter_rodentium_slice
  105. BIN t/data/rna_seq_bitwise_flags_set.bam
  106. BIN t/data/small_multi_sequence.bam
  107. BIN t/data/small_slice.bam
  108. 0 web_code/lookseq/lookseq.html
  109. +1 −0 web_code/lookseq/lookseq.js
  110. +149 −0 web_code/map-view/map_lanes_view.pl
  111. +51 −0 web_code/map-view/map_projects_view.pl
  112. +21 −394 web_code/map-view/map_view.pl
  113. +191 −0 web_code/pending-view/pending_requests_view.pl
  114. +21 −409 web_code/pending-view/pending_view.pl
  115. +0 −420 web_code/pending-view/pending_view2.pl
  116. +17 −10 web_code/qc_grind/study_lanes.pl
  117. +20 −542 web_code/sample-mapping/sample_mapping.pl
  118. +165 −0 web_code/sample-mapping/sample_mapping_lanes_view.pl
  119. +51 −0 web_code/sample-mapping/sample_mapping_projects_view.pl
  120. 0 web_code/snps/snps.css
  121. 0 web_code/snps/snps.js
View
@@ -26,7 +26,7 @@ use MyBuild;
my $build = MyBuild->new(
module_name => 'VertRes',
- dist_version => 0.03,
+ dist_version => 0.04,
dist_author => 'Vertebrate Resequencing group at the Sanger Institute',
dist_abstract => 'A collection of modules and scripts for processing and analysing large quantities of sequencing data.',
license => 'perl',
@@ -44,6 +44,7 @@ my $build = MyBuild->new(
'Net::FTP::Robust' => 0,
'Time::Format' => 0,
'IO::Capture::Stderr' => 0,
+ 'Math::Random' => 0,
},
pm_files => get_pm_files(),
script_files => 'scripts'
View
@@ -4,4 +4,6 @@ Version Description
------- -----------
0.01 Initial public release on github
0.02 Nice stable point, prior to an upcoming exome-related schema changes
-0.03 Stable point, known working for UK10K analysis, prior to incorporating many changes from Pathogens/HGI
+0.03 Stable point, known working for UK10K analysis, prior to incorporating
+ many changes from Pathogens/HGI
+0.04 VRTrack schema version 20, with the new AutoQC table
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