import VCF header #17
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Now irrelevant. |
danking
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# This is the 1st commit message: apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue # This is the commit message #2: convert relational.scala ; # This is the commit message #3: scope the extract aggregators constfb call # This is the commit message #4: scope interpret # This is the commit message #5: typeAfterSelect used by selectRegionValue # This is the commit message #6: load matrix # This is the commit message #7: imports # This is the commit message #8: loadbgen converted # This is the commit message #9: convert loadplink # This is the commit message #10: convert loadgdb # This is the commit message #11: convert loadvcf # This is the commit message #12: convert blockmatrix # This is the commit message #13: convert filterintervals # This is the commit message hail-is#14: convert ibd # This is the commit message hail-is#15: convert a few methods # This is the commit message hail-is#16: convert split multi # This is the commit message hail-is#17: convert VEP # This is the commit message hail-is#18: formatting fix # This is the commit message hail-is#19: add partitionBy and values # This is the commit message hail-is#20: fix bug in localkeysort # This is the commit message hail-is#21: fixup HailContext.readRowsPartition use # This is the commit message hail-is#22: port balding nichols model
danking
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May 4, 2018
* # This is a combination of 22 commits. # This is the 1st commit message: apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue # This is the commit message #2: convert relational.scala ; # This is the commit message #3: scope the extract aggregators constfb call # This is the commit message #4: scope interpret # This is the commit message #5: typeAfterSelect used by selectRegionValue # This is the commit message #6: load matrix # This is the commit message #7: imports # This is the commit message #8: loadbgen converted # This is the commit message #9: convert loadplink # This is the commit message #10: convert loadgdb # This is the commit message #11: convert loadvcf # This is the commit message #12: convert blockmatrix # This is the commit message #13: convert filterintervals # This is the commit message #14: convert ibd # This is the commit message #15: convert a few methods # This is the commit message #16: convert split multi # This is the commit message #17: convert VEP # This is the commit message #18: formatting fix # This is the commit message #19: add partitionBy and values # This is the commit message #20: fix bug in localkeysort # This is the commit message #21: fixup HailContext.readRowsPartition use # This is the commit message #22: port balding nichols model * apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue convert relational.scala ; scope the extract aggregators constfb call scope interpret typeAfterSelect used by selectRegionValue load matrix imports loadbgen converted convert loadplink convert loadgdb convert loadvcf convert blockmatrix convert filterintervals convert ibd convert a few methods convert split multi convert VEP formatting fix add partitionBy and values fix bug in localkeysort fixup HailContext.readRowsPartition use port balding nichols model port over table.scala couple fixes convert matrix table remove necessary use of rdd variety of fixups wip add a clear * Remove direct Region allocation from FilterColsIR When regions are off-heap, we can allow the globals to live in a separate, longer-lived Region that is not cleared until the whole partition is finished. For now, we pay the memory cost. * Use RVDContext in MatrixRead zip This Region will get cleared by consumers. I introduced the zip primitive which is a safer way to zip two RVDs because it does not rely on the user correctly clearing the regions used by the left and right hand sides of the zip. * Control the Regions in LoadGDB I do not fully understand how LoadGDB is working, but a simple solution to the use-case is to serialize to arrays of bytes and parallelize those. I realize there is a proliferation of `coerce` methods. I plan to trim this down once we do not have RDD and ContextRDD coexisting * wip * unify RVD.run * reset in write * fixes * use context region when allocating * also read RVDs using RVDContext * formatting * address comments * remove unused val * abstract over boundary * little fixes * whoops forgot to clear before persisting This fixes the LDPrune if you dont clear the region things go wrong. Not sure what causes that bug. Maybe its something about encoders? * serialize for shuffles, region.scoped in matrixmapglobals, fix joins * clear more! * wip * wip * rework GeneralRDD to ease ContextRDD transition * formatting * final fixes * formatting * merge failures * more bad merge stuff * formatting * remove unnecessary stuff * remove fixme * boom! * variety of merge mistakes * fix destabilize bug * add missing newline * remember to clear the producer region in localkeysort * switch def to val * cleanup filteralleles and exporbidbimfam * fix clearing and serialization issue * fix BitPackedVectorView Previously it always assumed the variant struct started at offset zero, which is not true * address comments, remove a comment * remove direct use of Region * oops * werrrks, mebbe * needs cleanup * fix filter intervals * fixes * fixes * fix filterintervals * remove unnecessary copy in TableJoin * and finally fix the last test * re-use existing CodecSpec definition * remove unnecessary boundaries * use RVD abstraction when possible * formatting * bugfix: RegionValue must know its region * remove unnecessary val and comment * remove unused methods * eliminate unused constructors * undo debug change * formatting * remove unused imports * fix bug in tablejoin * fix RichRDDSuite test If you have no data, then you have no partitions, not 1 partition
konradjk
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Jun 12, 2018
* # This is a combination of 22 commits. # This is the 1st commit message: apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue # This is the commit message #2: convert relational.scala ; # This is the commit message #3: scope the extract aggregators constfb call # This is the commit message hail-is#4: scope interpret # This is the commit message hail-is#5: typeAfterSelect used by selectRegionValue # This is the commit message hail-is#6: load matrix # This is the commit message hail-is#7: imports # This is the commit message hail-is#8: loadbgen converted # This is the commit message hail-is#9: convert loadplink # This is the commit message hail-is#10: convert loadgdb # This is the commit message hail-is#11: convert loadvcf # This is the commit message hail-is#12: convert blockmatrix # This is the commit message hail-is#13: convert filterintervals # This is the commit message hail-is#14: convert ibd # This is the commit message hail-is#15: convert a few methods # This is the commit message hail-is#16: convert split multi # This is the commit message hail-is#17: convert VEP # This is the commit message hail-is#18: formatting fix # This is the commit message hail-is#19: add partitionBy and values # This is the commit message hail-is#20: fix bug in localkeysort # This is the commit message hail-is#21: fixup HailContext.readRowsPartition use # This is the commit message hail-is#22: port balding nichols model * apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue convert relational.scala ; scope the extract aggregators constfb call scope interpret typeAfterSelect used by selectRegionValue load matrix imports loadbgen converted convert loadplink convert loadgdb convert loadvcf convert blockmatrix convert filterintervals convert ibd convert a few methods convert split multi convert VEP formatting fix add partitionBy and values fix bug in localkeysort fixup HailContext.readRowsPartition use port balding nichols model port over table.scala couple fixes convert matrix table remove necessary use of rdd variety of fixups wip add a clear * Remove direct Region allocation from FilterColsIR When regions are off-heap, we can allow the globals to live in a separate, longer-lived Region that is not cleared until the whole partition is finished. For now, we pay the memory cost. * Use RVDContext in MatrixRead zip This Region will get cleared by consumers. I introduced the zip primitive which is a safer way to zip two RVDs because it does not rely on the user correctly clearing the regions used by the left and right hand sides of the zip. * Control the Regions in LoadGDB I do not fully understand how LoadGDB is working, but a simple solution to the use-case is to serialize to arrays of bytes and parallelize those. I realize there is a proliferation of `coerce` methods. I plan to trim this down once we do not have RDD and ContextRDD coexisting * wip * unify RVD.run * reset in write * fixes * use context region when allocating * also read RVDs using RVDContext * formatting * address comments * remove unused val * abstract over boundary * little fixes * whoops forgot to clear before persisting This fixes the LDPrune if you dont clear the region things go wrong. Not sure what causes that bug. Maybe its something about encoders? * serialize for shuffles, region.scoped in matrixmapglobals, fix joins * clear more! * wip * wip * rework GeneralRDD to ease ContextRDD transition * formatting * final fixes * formatting * merge failures * more bad merge stuff * formatting * remove unnecessary stuff * remove fixme * boom! * variety of merge mistakes * fix destabilize bug * add missing newline * remember to clear the producer region in localkeysort * switch def to val * cleanup filteralleles and exporbidbimfam * fix clearing and serialization issue * fix BitPackedVectorView Previously it always assumed the variant struct started at offset zero, which is not true * address comments, remove a comment * remove direct use of Region * oops * werrrks, mebbe * needs cleanup * fix filter intervals * fixes * fixes * fix filterintervals * remove unnecessary copy in TableJoin * and finally fix the last test * re-use existing CodecSpec definition * remove unnecessary boundaries * use RVD abstraction when possible * formatting * bugfix: RegionValue must know its region * remove unnecessary val and comment * remove unused methods * eliminate unused constructors * undo debug change * formatting * remove unused imports * fix bug in tablejoin * fix RichRDDSuite test If you have no data, then you have no partitions, not 1 partition
jackgoldsmith4
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Jun 25, 2018
* # This is a combination of 22 commits. # This is the 1st commit message: apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue # This is the commit message hail-is#2: convert relational.scala ; # This is the commit message hail-is#3: scope the extract aggregators constfb call # This is the commit message hail-is#4: scope interpret # This is the commit message hail-is#5: typeAfterSelect used by selectRegionValue # This is the commit message hail-is#6: load matrix # This is the commit message hail-is#7: imports # This is the commit message hail-is#8: loadbgen converted # This is the commit message hail-is#9: convert loadplink # This is the commit message hail-is#10: convert loadgdb # This is the commit message hail-is#11: convert loadvcf # This is the commit message hail-is#12: convert blockmatrix # This is the commit message hail-is#13: convert filterintervals # This is the commit message hail-is#14: convert ibd # This is the commit message hail-is#15: convert a few methods # This is the commit message hail-is#16: convert split multi # This is the commit message hail-is#17: convert VEP # This is the commit message hail-is#18: formatting fix # This is the commit message hail-is#19: add partitionBy and values # This is the commit message hail-is#20: fix bug in localkeysort # This is the commit message hail-is#21: fixup HailContext.readRowsPartition use # This is the commit message hail-is#22: port balding nichols model * apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering make TrivialContext Resettable a few more missing resettablecontexts address comments apply resettable context forgot to fix one use of AutoCloseable fix add setup iterator more sensible method ordering remove rogue element type type make TrivialContext Resettable wip wip wip wip use safe row in join suite pull over hailcontext remove Region.clear(newEnd) add selectRegionValue convert relational.scala ; scope the extract aggregators constfb call scope interpret typeAfterSelect used by selectRegionValue load matrix imports loadbgen converted convert loadplink convert loadgdb convert loadvcf convert blockmatrix convert filterintervals convert ibd convert a few methods convert split multi convert VEP formatting fix add partitionBy and values fix bug in localkeysort fixup HailContext.readRowsPartition use port balding nichols model port over table.scala couple fixes convert matrix table remove necessary use of rdd variety of fixups wip add a clear * Remove direct Region allocation from FilterColsIR When regions are off-heap, we can allow the globals to live in a separate, longer-lived Region that is not cleared until the whole partition is finished. For now, we pay the memory cost. * Use RVDContext in MatrixRead zip This Region will get cleared by consumers. I introduced the zip primitive which is a safer way to zip two RVDs because it does not rely on the user correctly clearing the regions used by the left and right hand sides of the zip. * Control the Regions in LoadGDB I do not fully understand how LoadGDB is working, but a simple solution to the use-case is to serialize to arrays of bytes and parallelize those. I realize there is a proliferation of `coerce` methods. I plan to trim this down once we do not have RDD and ContextRDD coexisting * wip * unify RVD.run * reset in write * fixes * use context region when allocating * also read RVDs using RVDContext * formatting * address comments * remove unused val * abstract over boundary * little fixes * whoops forgot to clear before persisting This fixes the LDPrune if you dont clear the region things go wrong. Not sure what causes that bug. Maybe its something about encoders? * serialize for shuffles, region.scoped in matrixmapglobals, fix joins * clear more! * wip * wip * rework GeneralRDD to ease ContextRDD transition * formatting * final fixes * formatting * merge failures * more bad merge stuff * formatting * remove unnecessary stuff * remove fixme * boom! * variety of merge mistakes * fix destabilize bug * add missing newline * remember to clear the producer region in localkeysort * switch def to val * cleanup filteralleles and exporbidbimfam * fix clearing and serialization issue * fix BitPackedVectorView Previously it always assumed the variant struct started at offset zero, which is not true * address comments, remove a comment * remove direct use of Region * oops * werrrks, mebbe * needs cleanup * fix filter intervals * fixes * fixes * fix filterintervals * remove unnecessary copy in TableJoin * and finally fix the last test * re-use existing CodecSpec definition * remove unnecessary boundaries * use RVD abstraction when possible * formatting * bugfix: RegionValue must know its region * remove unnecessary val and comment * remove unused methods * eliminate unused constructors * undo debug change * formatting * remove unused imports * fix bug in tablejoin * fix RichRDDSuite test If you have no data, then you have no partitions, not 1 partition
cseed
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Sep 22, 2018
Removed headers on tables in the user page
danking
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Sep 24, 2018
* initial commit * changes to run on cluster * support multiple repos put token in kubenetes secrets * fixed deployment * fix ci fq repo name * updated Makefile use delete/create for redeploy until we stop using latest image * added custom user pages * fixed indentation * fix treating pulls as issues * poll Github * fix import * fix changes requested reporting * Small improvements - declare language="en" so I don't get translate notifications ????? - use defaultdict for great profit - use daemon thread so ctrl-C actually kills the server * fix * Small improvement 2 * add logging, restart on poll thread * fix users head/header * autoformat htmls (#12) * BANISH THE SERIFS WHENCE THEY CAME (#13) * add author column to "needs review" table (#14) * Add a list of failing builds to the user page (#16) * Slightly better formatting. (#17) Removed headers on tables in the user page * import sys so the retry stuff works (#18) * assertion is going off, log instead (#19) * reverse reviews (come in chrological order) (#20) We want the most recent. From https://developer.github.com/v3/pulls/reviews/: > The list of reviews returns in chronological order. scorecard was categorizing #4328 incorrectly. * move to project dir to merge into monorepo * updated .gitignore * backed off spacing * make targets phony
cseed
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May 1, 2019
Exposed --metadata and fixed problem with creating directory
danking
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Jul 8, 2019
Add annotation_db.json to hail-datasets
daniel-goldstein
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Feb 3, 2022
Conda pkg: prepare meta.yaml in a separate ubuntu job
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From @cseed on August 26, 2015 14:43
Store entire header. Parse contig at least. Expand
sampleIds: Array[String]to store metadata.Copied from original issue: cseed/hail#16
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