1. SeqVarTools
  2. Graph
Graph of SeqVarTools
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  • fa2a136 (HEAD -> devel, origin/master, origin/devel, origin/HEAD) bump x.y.z version to odd y following creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:28:13 -0400;
  • 5826906 (origin/RELEASE_3_17, RELEASE_3_17) bump x.y.z version to even y prior to creation of RELEASE_3_17 branch by J Wokaty <jwokaty@users.noreply.github.com> 2023-04-25 10:28:13 -0400;
  • 455dd5d fix man page warnings in R-devel by Stephanie M. Gogarten <sdmorris@uw.edu> 2022-12-16 00:15:09 -0800;
  • f138dd3 bump x.y.z version to odd y following creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:08:33 -0400;
  • be0bdfb (origin/RELEASE_3_16, RELEASE_3_16) bump x.y.z version to even y prior to creation of RELEASE_3_16 branch by J Wokaty <jennifer.wokaty@sph.cuny.edu> 2022-11-01 11:08:33 -0400;
  • 58494fa correct for seqAlleleCount returning NA when no samples selected by Stephanie M. Gogarten <sdmorris@uw.edu> 2022-06-28 10:36:00 -0700;
  • b7b75a0 bump x.y.z version to odd y following creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:15:50 +0000;
  • 5506e93 (origin/RELEASE_3_15, RELEASE_3_15) bump x.y.z version to even y prior to creation of RELEASE_3_15 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2022-04-26 15:15:50 +0000;
  • 06f4830 bump x.y.z version to odd y following creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:09:17 +0000;
  • 311c07d (origin/RELEASE_3_14, RELEASE_3_14) bump x.y.z version to even y prior to creation of RELEASE_3_14 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-10-26 16:09:17 +0000;
  • a59290c bump x.y.z version to odd y following creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:00:00 +0000;
  • 0617a90 (origin/RELEASE_3_13, RELEASE_3_13) bump x.y.z version to even y prior to creation of RELEASE_3_13 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2021-05-19 16:00:00 +0000;
  • c109b54 allow sex values to be character 1,2 by Stephanie M. Gogarten <sdmorris@uw.edu> 2021-02-18 13:44:33 -0800;
  • f6ac0e6 fix man page lines too long for pdf manual by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-11-23 09:17:37 -0800;
  • f5e7670 version bump by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-11-19 23:37:02 -0800;
  • 54a8fd7 (origin/RELEASE_3_12, RELEASE_3_12) version bump by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-11-19 23:35:51 -0800;
  • f493cd2 parallel=TRUE doesn't work for by.sample by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-11-19 23:31:20 -0800;
  • 5ccf9d3 parallel=TRUE doesn't work for by.sample by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-11-19 23:31:20 -0800;
  • d26df12 bump x.y.z version to odd y following creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:52:06 -0400;
  • f0abda9 bump x.y.z version to even y prior to creation of RELEASE_3_12 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-10-27 10:52:06 -0400;
  • f6f0bb1 replace tidyverse with data.table in variantInfo by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-09-29 21:34:42 -0700;
  • faeec71 clarify docs for SeqVarData by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-05-18 17:22:04 -0700;
  • 5332108 add parallel argument to methods by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-05-18 16:49:47 -0700;
  • e4213a6 bump x.y.z version to odd y following creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:35:48 +0000;
  • e0344d7 (origin/RELEASE_3_11, RELEASE_3_11) bump x.y.z version to even y prior to creation of RELEASE_3_11 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2020-04-27 18:35:48 +0000;
  • ff414b7 change in how SeqArray returns variable length data by smgogarten <sdmorris@uw.edu> 2020-04-06 12:51:33 -0700;
  • bfb4f6b version bump by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-03-16 17:00:17 -0700;
  • a7897b8 keep allele count as integer when possible by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-03-16 16:53:53 -0700;
  • f0ee218 (origin/RELEASE_3_10, RELEASE_3_10) version bump by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-03-16 14:43:47 -0700;
  • d6196cc Bug fix: .nSampObserved with no samples by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-03-16 13:21:44 -0700;
  • dba3d8d Bug fix: .nSampObserved with no samples by Stephanie M. Gogarten <sdmorris@uw.edu> 2020-03-16 13:21:44 -0700;
  • a952bd0 bump x.y.z version to odd y after creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:36:54 -0400;
  • b528ef9 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-10-29 13:08:45 -0400;
  • 8205651 use SeqArray method for returning reference allele dosage by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-07-16 12:56:18 -0700;
  • a4b5b0b add check for whether males are coded as diploid by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-07-16 09:45:45 -0700;
  • 23e103d move code for MAC ignoring sex to separate method for SeqVarGDSClass by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-07-11 21:01:13 -0700;
  • 8cd8559 add minorAlleleCount method by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-07-11 17:30:04 -0700;
  • e2e9bcd (origin/RELEASE_3_9, RELEASE_3_9) use set.seed for deterministic unit tests by smgogarten <smgogarten@velasca> 2019-05-09 15:37:15 -0700;
  • f1c3503 use set.seed for deterministic unit tests by smgogarten <smgogarten@velasca> 2019-05-09 15:37:15 -0700;
  • bd8937f bump x.y.z versions to odd y after creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 12:11:25 -0400;
  • a8b0298 bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch by Nitesh Turaga <nitesh.turaga@gmail.com> 2019-05-02 11:53:44 -0400;
  • 390dfa2 getGenotype* methods now work on haploid genotypes with no phase by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-04-22 14:07:53 -0700;
  • 1987535 update README by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-04-22 11:24:23 -0700;
  • c81f10d add vignette describing iterators by smgogarten <smgogarten@velasca> 2019-04-11 17:25:38 -0700;
  • 320b99c seqBlockApply is slower than seqApply with larger datasets by smgogarten <smgogarten@velasca> 2019-04-11 16:01:29 -0700;
  • 33b95c1 use seqBlockApply instead of seqApply in getGenotype* methods by smgogarten <smgogarten@velasca> 2019-04-11 14:54:23 -0700;
  • d986786 use ZIP compression instead of LZMA in dosage example by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-03-06 15:46:45 -0800;
  • 92fe035 (origin/RELEASE_3_8, RELEASE_3_8) version bump by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-02-26 13:05:10 -0800;
  • 1b7b641 bug fix: include variants with no alt alleles in expanded view by smgogarten <smgogarten@velasca> 2019-02-26 13:00:58 -0800;
  • ae4b627 version bump by smgogarten <smgogarten@velasca> 2019-02-26 13:02:54 -0800;
  • 6692124 bug fix: include variants with no alt alleles in expanded view by smgogarten <smgogarten@velasca> 2019-02-26 13:00:58 -0800;
  • 77bdd8f update for changes in dplyr 0.8.0 by smgogarten <smgogarten@velasca> 2019-01-29 13:42:20 -0800;
  • aac15dc update for changes in dplyr 0.8.0 by smgogarten <smgogarten@velasca> 2019-01-29 13:42:20 -0800;
  • 47d2a85 version bump by smgogarten <smgogarten@velasca> 2019-01-17 12:22:04 -0800;
  • a61afe9 Merge pull request <a href="#1">#1</a> from smgogarten/dosage by Stephanie M. Gogarten <sdmorris@uw.edu> 2019-01-17 12:18:17 -0800;
  • 1c07724 add method to read dosage from DS field by smgogarten <smgogarten@velasca> 2018-12-05 10:34:19 -0500;
  • 4899f4e bump x.y.z versions to odd y after creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:54:31 -0400;
  • 37ee964 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch by vobencha <vobencha@gmail.com> 2018-10-30 11:41:51 -0400;
  • b38fc9e update documentation and NEWS by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-10-19 13:15:23 -0700;
  • 448283c reduce memory usage when creating a SeqVarData object by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-09-21 14:51:19 -0700;
  • 5c7ce3a Merge branch 'dupdisc' Improve calculations of duplicate discordance within a single GDS file by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 14:51:31 -0700;
  • 7016a49 deal with blocks of 1 variant by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 14:49:40 -0700;
  • cc9bbcd use Reduce instead of do.call for >2 elements by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 11:36:35 -0700;
  • c5f207d remove NA from the list of subject IDs to match by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 10:50:09 -0700;
  • f19b46b add duplicateDiscordance method for SeqVarIterator by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 09:33:27 -0700;
  • f4c5efb add resetIterator method by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-08-08 09:32:30 -0700;
  • bd7051c duplicateDiscordance on a single gds file does alt allele conc by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-07-10 10:36:54 -0700;
  • 0ca28ab add currentVariants to man page by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-06-25 11:52:31 -0700;
  • dfb468c add currentVariants methods by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-06-21 15:38:07 -0700;
  • 1029005 fix failing unit test - integer/character row names by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-06-11 14:12:28 -0700;
  • 4096c33 added github URL by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-05-30 10:36:45 -0700;
  • 31b761a bump x.y.z versions to odd y after creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:41:39 -0400;
  • 2fc39e9 (origin/RELEASE_3_7, RELEASE_3_7) bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch by vobencha <valerie.obenchain@roswellpark.org> 2018-04-30 10:35:31 -0400;
  • e24e8ad fix unit test with new RLE indexing in SeqArray chromosome node by smgogarten <smgogarten@velasca> 2018-04-19 09:56:47 -0700;
  • d2d8a7e added unit test for duplicate variants in an iterator by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-04-18 15:11:54 -0700;
  • f36f8e4 added alleleCount method by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-03-20 17:27:26 -0700;
  • 20e0b62 version bump and NEWS for bug fix by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-03-16 18:14:02 -0700;
  • eea11aa (origin/RELEASE_3_6, RELEASE_3_6) version bump and NEWS for bug fix by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-03-16 18:12:27 -0700;
  • 255e8a7 Bux fix in alleleFrequency method for SeqVarData by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-03-16 18:06:11 -0700;
  • f7d070d Bux fix in alleleFrequency method for SeqVarData by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-03-16 18:06:11 -0700;
  • 8688525 update NEWS by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-02-27 09:55:00 -0800;
  • a0fabf9 use named argument for variant.sel by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-02-15 10:51:05 -0800;
  • 57e45f2 Merge branch 'feature-sparse_matrix' by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-26 15:11:32 -0800;
  • 36ce8ff pass sparse arg from expandedAltDosage to altDosage by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-26 11:55:49 -0800;
  • 232df71 explicit links to SeqArray package in man page are unnecessary by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-18 10:46:29 -0800;
  • 28660d9 use sparse matrices for alt dosage by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-16 15:09:47 -0800;
  • c953954 use seqBlockApply instead of seqApply for reading dosages by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-16 12:13:13 -0800;
  • 47a0383 add show methods by Stephanie M. Gogarten <sdmorris@uw.edu> 2018-01-05 12:23:29 -0800;
  • 6c8247f Merge remote-tracking branch 'origin/master' by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-12-22 16:04:28 -0800;
  • 605d6d0 added currentRanges method by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-12-22 16:03:10 -0800;
  • aa12be9 Update README.md by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-12-19 11:27:54 -0800;
  • 1af5369 variantInfo uses abbreviations chr,pos in column names by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-12-11 14:16:29 -0800;
  • a9c47d2 add news and clean up commented-out code by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-12-08 09:00:16 -0800;
  • fc07d11 store indices of variant filters in iterator object by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-11-28 14:34:23 -0800;
  • 7cd40bc deal with number of variants < variantBlock by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-11-27 10:09:28 -0800;
  • 360218f bump x.y.z versions to odd y after creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:52:52 -0400;
  • 0aba387 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch by Hervé Pagès <hpages@fredhutch.org> 2017-10-30 12:40:06 -0400;
  • 5f8fda5 add method to identify PAR, fix names in alleleFrequency by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-09-25 12:00:22 -0700;
  • 53a6989 add option to exclude PAR from sex-specific allele frequency by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-09-21 12:57:09 -0700;
  • df534e5 account for sex in alleleFrequency on X and Y chroms by Stephanie M. Gogarten <sdmorris@uw.edu> 2017-09-20 16:08:26 -0700;