diff --git a/build.xml b/build.xml index 224bb6417..265bc6f83 100644 --- a/build.xml +++ b/build.xml @@ -83,11 +83,7 @@ - - - - - + @@ -471,7 +467,7 @@ - + diff --git a/doc/Genome Analysis TK plan.omniplan/contents.xml b/doc/Genome Analysis TK plan.omniplan/contents.xml deleted file mode 100644 index 8e803574c..000000000 --- a/doc/Genome Analysis TK plan.omniplan/contents.xml +++ /dev/null @@ -1,2594 +0,0 @@ - - - - - baseStyle - - font-family - Lucida Grande - - columnTitleStyle - - font-size - 13 - font-weight - 9 - paragraph-alignment - center - - cost - 0.0 - currencyStyle - $1,234.56 - displayDates - - displayProperties - - - GanttGroupShading - - GanttVisibleRect - {{1132, 0}, {1025, 950}} - OutlineVisibleRect - {{0, 0}, {789, 950}} - ScaleWidths - - Automatic - 100 - Day - 405 - Hour - 21960 - Minute - 21600 - Month - 11.5 - Quarter - 3.2000000476837158 - Week - 54 - Year - 0.78749996423721313 - - SelectedPlanView - 1 - SelectedScale - Week - SelectedView - 0 - SheetSettings - - LevelConstrainsCompletionDate - - LevelUpdatesSelectedTasks - - RescheduleUpdatesSelectedTasks - - - ShouldDrawFolded - - ShowConstraints - - ShowCriticalPath - - ShowDependencyLines - - ShowGanttTimeOff - - activeColumnIdentifiers - - Violations - Notes - Title - Effort - %Done - - calendarController - - OutlineVisibleRect - {{0, 0}, {571, 747}} - activeColumnIdentifiers - - IM - Notes - Type - Resource - Custom Work Week - Schedule Exception - - columnWidths - - IM - 20 - Notes - 20 - Resource - 436 - Type - 48 - - - calendarSplit - 0.67960631847381592 - columnWidths - - Effort - 70 - Notes - 20 - Title - 580 - Violations - 20 - - dayWidth - 54 - resourceSplit - 0.56752324104309082 - resourcesController - - DayWidth - 25 - OutlineVisibleRect - {{0, 0}, {776, 950}} - ScaleWidths - - Automatic - 25 - Day - 405 - Hour - 21960 - Minute - 21600 - Month - 11.5 - Quarter - 3.2000000476837158 - Week - 54 - Year - 0.78749996423721313 - - SelectedScale - Automatic - TimelineVisibleRect - {{-1467, 0}, {995, 950}} - activeColumnIdentifiers - - IM - Notes - Type - Resource - # - - columnWidths - - # - 75 - IM - 20 - Notes - 20 - Resource - 591 - Type - 64 - - - side - 0.56861674785614014 - window - {{48, 62}, {1838, 1087}} - - - displaySeconds - - displayStatusCompletion - - displayStatusCost - - displayStatusEndDate - - displayStatusStartDate - - displayStatusTitle - - displayTimes - - endDate - 20090424 15:45 - flatNumbering - - groupTaskStyle - - font-size - 13 - font-weight - 9 - - notEditableStyle - - font-fill - - w - 0.334677 - - - noteStyle - - font-family - Helvetica - font-fill - - w - 0.334677 - - font-italic - - - objectId - 0 - printInfo - - NSOrientation - 0 - NSPaperName - na-letter - NSPrinterName - dahl - NSScalingFactor - 1 - OPPrintSettingPrintDisplayOption - 0 - OPPrintSettingPrintOption - 0 - - projectUserKeys - - resourceDifferenceEngine - - nextId - 24 - - resourceUserKeys - - resources - - - available - 5.9499998092651367 - children - - 1 - 5 - 10 - 14 - 16 - - efficiency - 0.59499996900558472 - objectId - -1 - type - 3 - - - available - 2 - children - - 2 - 3 - - name - Software Engineering team - objectId - 1 - type - 3 - - - name - Matthew Hanna - objectId - 2 - - - name - Aaron McKenna - objectId - 3 - - - children - - 6 - 7 - 8 - 9 - - efficiency - 0.25 - name - Computational Biologists - objectId - 5 - type - 3 - - - available - 0.25 - name - Kiran Garimella - objectId - 6 - - - available - 0.25 - name - Andrey Sivachenko - objectId - 7 - - - available - 0.25 - name - Andrew Kernytsky - objectId - 8 - - - available - 0.25 - name - Eric Banks - objectId - 9 - - - available - 0.94999998807907104 - children - - 11 - 12 - - efficiency - 0.47499999403953552 - name - Group leaders - objectId - 10 - type - 3 - - - available - 0.75 - name - Mark DePristo - objectId - 11 - - - available - 0.19999998807907104 - name - Jared Maguire - objectId - 12 - - - name - Production informatics team - objectId - 14 - - - name - MPG software engineering - objectId - 16 - - - schedule - - friday - - spans - - - endTime - 43200 - startTime - 28800 - - - endTime - 61200 - startTime - 46800 - - - - monday - - spans - - - endTime - 43200 - startTime - 28800 - - - endTime - 61200 - startTime - 46800 - - - - saturday - - sunday - - thursday - - spans - - - endTime - 43200 - startTime - 28800 - - - endTime - 61200 - startTime - 46800 - - - - tuesday - - spans - - - endTime - 43200 - startTime - 28800 - - - endTime - 61200 - startTime - 46800 - - - - wednesday - - spans - - - endTime - 43200 - startTime - 28800 - - - endTime - 61200 - startTime - 46800 - - - - - scheduleGranularity - 0 - sharedFormatter - - displayDays - - displayHours - - displayMinutes - - displayMonths - - displaySeconds - - displayWeeks - - displayYears - - hoursPerDay - 8 - hoursPerMonth - 160 - hoursPerWeek - 40 - hoursPerYear - 1920 - - startDate - 20090315 00:00 - taskBarLabels - - Gantt View - - taskTypeGroup - - OPGanttLeftTextKey - - OPGanttOverTextKey - - OPGanttRightTextKey - Assigned - - taskTypeMilestone - - OPGanttLeftTextKey - - OPGanttOverTextKey - - OPGanttRightTextKey - Assigned - - taskTypeTask - - OPGanttLeftTextKey - - OPGanttOverTextKey - - OPGanttRightTextKey - Assigned - - - Timeline View - - taskTypeGroup - - OPGanttLeftTextKey - Title - OPGanttOverTextKey - - OPGanttRightTextKey - - - taskTypeMilestone - - OPGanttLeftTextKey - Title - OPGanttOverTextKey - - OPGanttRightTextKey - Assigned - - taskTypeTask - - OPGanttLeftTextKey - Title - OPGanttOverTextKey - - OPGanttRightTextKey - - - - - taskDifferenceEngine - - nextId - 131 - - taskUserKeys - - tasks - - - children - - 55 - 32 - 56 - 23 - 84 - 27 - 50 - - objectId - -1 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 86400 - effort - 86400 - effortDone - 86400 - objectId - 1 - style - - font-size - 12 - - task - Select canonical build system, with eye for easy construction of publically available library and software tools - workDone - 24 - workSeconds - 86400 - workTime - 24 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 3 - prerequisites - - - id - 1 - kind - 2 - - - style - - font-size - 12 - - task - Documentation on how to configure and develop in environment - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - children - - 52 - 53 - - objectId - 5 - style - - font-size - 12 - - task - Extensible command line argument system - - - effort - 14400 - objectId - 6 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - ByLoci traversal -- need flag to include all reference loci, not just those covered by reads - workSeconds - 14400 - workTime - 4 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 57600 - effort - 57600 - effortDone - 57600 - objectId - 7 - style - - font-size - 12 - - task - Indexing of BAM files -- access BAM index file and support jumping around - workDone - 16 - workSeconds - 57600 - workTime - 16 - - - effort - 28800 - objectId - 8 - style - - font-size - 12 - gantt-fill-color - - b - 0.907362 - g - 0.615564 - r - 0.437675 - - - task - Develop algorithm for indexing of reference ordered data - workSeconds - 28800 - workTime - 8 - - - children - - 98 - 97 - - forcedStart - 20090331080000 - objectId - 9 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - ByReference traversal - - - assignments - - - id - 11 - units - 0.25 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 7200 - objectId - 10 - style - - font-size - 12 - - task - Handle argument type checking -- throw errors for bad types -- handle problem with providing arguments to flag causing problems everywhere - workDone - 8 - workSeconds - 115200 - workTime - 32 - - - effort - 28800 - objectId - 11 - style - - font-size - 12 - - task - Improve performance of BAM reader, BinaryCodec is slow - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 12 - prerequisites - - - id - 73 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.907362 - g - 0.615564 - r - 0.437675 - - - task - ROD writer -- in particular GFF for allele caller - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 13 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Provide external access to TraversalEngine data structures so that we can write algorithms that use reads, reference, rods outside of the walker system but using the AnalysisTK interface and loading routines. - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 15 - prerequisites - - - id - 12 - kind - 2 - - - id - 26 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.907362 - g - 0.615564 - r - 0.437675 - - - task - On disk sorting of RODs -- see reading all data in memory in PrepareROD - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 16 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Enable window size in traversal -- N bases for loci, for example - workSeconds - 28800 - workTime - 8 - - - effort - 86400 - objectId - 17 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - ByPair traversal -- ordered and unordered - workSeconds - 86400 - workTime - 24 - - - effort - 28800 - objectId - 18 - prerequisites - - - id - 7 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Random Loci - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 19 - prerequisites - - - id - 18 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Random Reads - workSeconds - 28800 - workTime - 8 - - - children - - 73 - 93 - 74 - 8 - 26 - 12 - 15 - 61 - - objectId - 23 - style - - font-size - 12 - gantt-fill-color - - b - 0.907362 - g - 0.615564 - r - 0.437675 - - - task - Reference ordered data - - - effort - 28800 - forcedStart - 20090317080000 - objectId - 26 - prerequisites - - - id - 8 - kind - 2 - - - id - 73 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.907362 - g - 0.615564 - r - 0.437675 - - - task - Jumping around in RODs - workSeconds - 28800 - workTime - 8 - - - children - - 6 - 9 - 17 - 49 - 16 - 13 - 94 - - objectId - 27 - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Traversal algorithms - - - children - - 121 - 91 - 103 - 113 - 125 - 126 - 120 - - objectId - 32 - style - - font-size - 12 - - task - Traversal engine generalization - - - effort - 28800 - objectId - 33 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Resumable walker support -- Serialization and state saving of traversal engine - workSeconds - 28800 - workTime - 8 - - - children - - 18 - 109 - 19 - 37 - 33 - 38 - 39 - 40 - - objectId - 36 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Long-term projects - - - effort - 28800 - objectId - 37 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Parallelization and chunking -- automatic parallelization -- how?  I/O? Hapdoop? LSF - workSeconds - 28800 - workTime - 8 - - - doneSeconds - 57600 - effort - 57600 - effortDone - 57600 - forcedStart - 20090413080000 - objectId - 38 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Internal bug tracking -- catching errors and posting them to data for tracking? - workDone - 16 - workSeconds - 57600 - workTime - 16 - - - effort - 28800 - objectId - 39 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Interfacing Java and Python -- how?  Want to write walkers in python for rapid prototyping - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 40 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Support for communal directory and naming system for reference ordered data -- I don't want to always have to provide command line flag for DBSNP when a walker needs it.  How do we we this? - workSeconds - 28800 - workTime - 8 - - - children - - 44 - 46 - 47 - 78 - 79 - 80 - 83 - 95 - 96 - 111 - - objectId - 41 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Short-term projects / bugs - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 43 - style - - font-size - 12 - - task - Need a better way to dynamically tell the class of a walker instead of trying to cast it and catching the exception - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 44 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Optimize GenomeLoc so that comparison operations are cheaper. Right now we use contig strings (painful) and really should automatically index / intern the strings upon creation for fast comparisons. Maybe build fast lookup system with regex? - workSeconds - 28800 - workTime - 8 - - - children - - 58 - 59 - - isExpanded - - objectId - 45 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Faster loading of fasta file - - - effort - 28800 - objectId - 46 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Fix: NullPointerException at sting.utils.Utils.setupRefContigOrdering.  When I leave out the reference, I get a SAMFormatException (I think because it defaults to expecting paired reads) - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 47 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Time per read base in performance output - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 49 - prerequisites - - - id - 17 - kind - 2 - - - style - - font-size - 12 - gantt-fill-color - - b - 0.898039 - g - 0.792157 - r - 0.219608 - - - task - Spanning pairs traversal - workSeconds - 28800 - workTime - 8 - - - children - - 41 - 36 - - objectId - 50 - style - - font-size - 12 - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Proposed features - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 52 - task - Choose replacement - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 53 - prerequisites - - - id - 52 - kind - 2 - - - task - Add replacement code to project - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 86400 - effort - 86400 - effortDone - 86400 - forcedStart - 20090324080000 - objectId - 54 - prerequisites - - - id - 53 - kind - 2 - - - task - Extend walkers to support extra arguments - workDone - 24 - workSeconds - 86400 - workTime - 24 - - - children - - 3 - 5 - 71 - 1 - 10 - 45 - 106 - 63 - - objectId - 55 - style - - font-size - 12 - - task - Software engineering infrastructure - - - children - - 7 - 11 - - objectId - 56 - style - - font-size - 12 - - task - SAM/BAM Support - - - assignments - - - id - 14 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 58 - style - - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Faster reads - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 11 - units - 0.75 - - - doneSeconds - 19200 - effort - 14400 - effortDone - 14400 - objectId - 59 - prerequisites - - - id - 58 - kind - 2 - - - style - - gantt-fill-color - - b - 0.101961 - g - 0.101961 - r - 0.101961 - - - task - Enable fast jumping to offset in fasta file by calculating minimum offset for next contig from dictionary - workDone - 5.3333334922790527 - workSeconds - 19200 - workTime - 5.3333334922790527 - - - effort - 28800 - objectId - 61 - prerequisites - - - id - 15 - kind - 2 - - - task - Revised preprocessing algorithm for ROD incorporating new indexing and sorting systems - workSeconds - 28800 - workTime - 8 - - - children - - 70 - 64 - 65 - 68 - - objectId - 63 - task - Quality assurance and stress testing - - - effort - 28800 - objectId - 64 - prerequisites - - - id - 70 - kind - 2 - - - task - Expand simple python script to handle more detailed list of BAM files to process, along with additional commands to execute the data on - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 65 - prerequisites - - - id - 64 - kind - 2 - - - task - Continue integration of stress test requests into a unified list - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 68 - prerequisites - - - id - 65 - kind - 2 - - - task - Enable tracking of results in GATK -- needs a stress test mode that will email if something fails - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 11 - units - 0.75 - - - effort - 28800 - objectId - 70 - task - Develop preliminary stress test system -- enable weekly testing of many files in common (CountReads, Pileup, etc.) to ensure the system can process files - workSeconds - 38400 - workTime - 10.666666984558105 - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 71 - task - Logging system support - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 73 - task - Revise the reference metadata system, really think about the organization from scratch. A key issue will be dynamic loading of RMD, we need a mime like system and ways of registering handlers - workSeconds - 28800 - workTime - 8 - - - effort - 3600 - objectId - 74 - task - Rename to reference metadata, not ROD - workSeconds - 3600 - workTime - 1 - - - effort - 28800 - objectId - 78 - task - Add support for "and onward" argument to location, so we can say "chr1:1+" will start from chr1 and continue onward for the rest of the file - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 2 - units - 1 - - - effort - 3600 - objectId - 79 - task - Move interval interface into Picard - workSeconds - 3600 - workTime - 1 - - - assignments - - - id - 7 - units - 0.25 - - - effort - 7200 - objectId - 80 - task - Utilize Picard interval and expand functionality if at all possible - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 83 - task - The file progress meter is stupidly broken on lane /seq/dirseq/aphilipp/combo/sequences/pcr/samfiles/9701.7.clean.sam in CountReads mode - workSeconds - 28800 - workTime - 8 - - - children - - 43 - 85 - 88 - - forcedStart - 20090323080000 - objectId - 84 - task - Walker infrastructure - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - forcedStart - 20090330080000 - objectId - 85 - prerequisites - - - id - 43 - kind - 2 - - - task - Loading of walkers from external Jar file - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - forcedStart - 20090326080000 - objectId - 86 - task - Generalized walker class hierarchy - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - children - - 54 - 86 - 90 - - objectId - 88 - task - Feature rich base walker class - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - forcedStart - 20090327080000 - objectId - 90 - task - Output stream in walker for use in map/reduce - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 172800 - effort - 172800 - effortDone - 172800 - forcedStart - 20090323080000 - objectId - 91 - task - Separate traversal type, data sources, and execution managers into separate object hierarchy - workDone - 48 - workSeconds - 172800 - workTime - 48 - - - effort - 28800 - objectId - 93 - task - Develop sound, common core of RMD types, unify work of kris, andrew, etc. on affy type. Look into what tim has done. - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 94 - task - Upgrade interval traversals.  Allow nested / overlapping, etc. intervals, along with map getting info on our interval (pass in genomeLoc) and reduce receiving all of the map results over that interval. Handle RODs and Reference appropriately. - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 95 - task - itertools for java - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 96 - task - Generalize file line reading (readlines and xreadlines) and use it for parsing locations, etc - workSeconds - 28800 - workTime - 8 - - - doneSeconds - 28800 - effort - 28800 - effortDone - 28800 - objectId - 97 - prerequisites - - - id - 98 - kind - 2 - - - task - General discovery + genotyping concordance tool - workDone - 8 - workSeconds - 28800 - workTime - 8 - - - doneSeconds - 57600 - effort - 57600 - effortDone - 57600 - objectId - 98 - task - Development and testing of ByReference traversal - workDone - 16 - workSeconds - 57600 - workTime - 16 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 43200 - effort - 43200 - effortDone - 43200 - forcedStart - 20090402080000 - objectId - 103 - task - Create basic by locus threading prototype - workDone - 12 - workSeconds - 43200 - workTime - 12 - - - children - - 107 - 108 - - forcedStart - 20090323080000 - objectId - 106 - task - Dynamic merging of multiple input BAM files into single stream - - - assignments - - - id - 11 - units - 0.75 - - - doneSeconds - 38400 - effort - 28800 - effortDone - 28800 - objectId - 107 - task - Basic code support - workDone - 10.666666984558105 - workSeconds - 38400 - workTime - 10.666666984558105 - - - assignments - - - id - 3 - units - 1 - - - effort - 28800 - objectId - 108 - task - Support in new data shard system - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 109 - task - Add mapping function from dict -> dict so we can process 1KG data against HS_18 assembly - workSeconds - 28800 - workTime - 8 - - - effort - 28800 - objectId - 111 - task - Fix rodDBSNP - workSeconds - 28800 - workTime - 8 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 115200 - effort - 115200 - effortDone - 115200 - forcedStart - 20090406130000 - objectId - 113 - task - Implement sharded single-threaded by reference traversal in with MicroManager - workDone - 32 - workSeconds - 115200 - workTime - 32 - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 139950 - effort - 279900 - effortDone - 139950 - forcedStart - 20090413090000 - objectId - 120 - prerequisites - - - id - 113 - kind - 2 - - - id - 121 - kind - 2 - - - task - Unit test of the shattering and parallel prototype 0 code - workDone - 38.875 - workSeconds - 279900 - workTime - 77.75 - - - assignments - - - id - 3 - units - 1 - - - doneSeconds - 172260 - effort - 198000 - effortDone - 172260 - forcedStart - 20090402080000 - objectId - 121 - prerequisites - - - id - 91 - kind - 2 - - - task - Create read and loci order shattering strategies - workDone - 47.849998474121094 - workSeconds - 198000 - workTime - 55 - - - assignments - - - id - 2 - units - 1 - - - doneSeconds - 57600 - effort - 57600 - effortDone - 57600 - forcedStart - 20090413080000 - objectId - 125 - task - Create and test stateless fasta file reader - workDone - 16 - workSeconds - 57600 - workTime - 16 - - - effort - 86400 - forcedStart - 20090420081500 - objectId - 126 - task - Integrate parallelism code into sharded MicroManager - workSeconds - 86400 - workTime - 24 - - - topResources - - -1 - - topTasks - - -1 - - uuid - 576AFD44-5E1C-4722-A13C-81450FCA5F4F - version - 2 - - diff --git a/ivy.xml b/ivy.xml index cebf26a86..ba02d9b6b 100644 --- a/ivy.xml +++ b/ivy.xml @@ -19,7 +19,7 @@ - + diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java index 4fe8a6cec..744b3fcdb 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java @@ -25,12 +25,15 @@ package org.broadinstitute.sting.utils.classloader; -import org.reflections.Reflections; -import org.reflections.scanners.ResourcesScanner; -import org.reflections.scanners.SubTypesScanner; -import org.reflections.util.ConfigurationBuilder; -import org.reflections.util.ManifestAwareClasspathHelper; +import ch.qos.logback.classic.Level; +import ch.qos.logback.classic.Logger; +import ch.qos.logback.classic.LoggerContext; import org.broadinstitute.sting.utils.StingException; +import org.reflections.Reflections; +import org.reflections.scanners.SubTypesScanner; +import org.reflections.util.ClasspathHelper; +import org.reflections.util.ConfigurationBuilder; +import org.slf4j.LoggerFactory; import java.net.URL; import java.util.Set; @@ -41,18 +44,21 @@ import java.util.List; * PackageUtils contains some useful methods for package introspection. */ public class PackageUtils { - + /** * A reference into our introspection utility. */ private static Reflections reflections = null; static { - List urls = ManifestAwareClasspathHelper.getUrlsForManifestCurrentClasspath(); + // turn off logging in the reflections library - they talk too much (to the wrong logger factory as well, logback) + Logger logger = (ch.qos.logback.classic.Logger)LoggerFactory.getLogger(Reflections.class); + logger.setLevel(Level.OFF); + // Initialize general-purpose source tree reflector. reflections = new Reflections( new ConfigurationBuilder() - .setUrls(urls) - .setScanners(new SubTypesScanner(),new ResourcesScanner())); + .setUrls(getClassPathURLs()) + .setScanners(new SubTypesScanner())); } /** @@ -115,4 +121,8 @@ public class PackageUtils { return nonConcreteTypes; } + + public static Set getClassPathURLs() { + return ClasspathHelper.getUrlsForCurrentClasspath(); + } } diff --git a/scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala b/scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala index 36bc97a7c..a55bb8ee4 100755 --- a/scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala +++ b/scala/src/org/broadinstitute/sting/queue/util/ClasspathUtils.scala @@ -1,7 +1,7 @@ package org.broadinstitute.sting.queue.util import collection.JavaConversions._ -import org.reflections.util.ManifestAwareClasspathHelper +import org.broadinstitute.sting.utils.classloader.PackageUtils import java.io.File import javax.print.URIException import java.net.{URL, URLClassLoader} @@ -16,7 +16,7 @@ object ClasspathUtils { * @return List[File] that build up the current classpath. */ def manifestAwareClassPath = { - var urls = ManifestAwareClasspathHelper.getUrlsForManifestCurrentClasspath + var urls = PackageUtils.getClassPathURLs urls.map(url => try {new File(url.toURI)} catch {case urie: URIException => new File(url.getPath)}) } @@ -33,3 +33,4 @@ object ClasspathUtils { method.invoke(ClassLoader.getSystemClassLoader(), url); } } + diff --git a/settings/ivysettings.xml b/settings/ivysettings.xml index e5f39d0f2..383882a2a 100644 --- a/settings/ivysettings.xml +++ b/settings/ivysettings.xml @@ -9,12 +9,13 @@ + - + diff --git a/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.jar b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.jar deleted file mode 100644 index d9265c204..000000000 Binary files a/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.jar and /dev/null differ diff --git a/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.xml b/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.xml deleted file mode 100644 index 75fd688fb..000000000 --- a/settings/repository/org.reflections/reflections-0.9.5-svnversion79M_mod2.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - -