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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 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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