Commits for kent

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

d32a1c4535597376154d2e4726edceb34a7b1612 Tue Oct 8 15:28:26 2019 -0700

• Addressing feedback in issues 1-5 including rearrangements of Projects page, renaming AssayTech to CdnaLibraryPrep, adding doc strings to the models in models.py, making project title and a few other fields get more space.
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 44, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/api.py - lines changed 9, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/api_urls.py - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 42, context: html, text, full: html, text

c83c7ebf5494774741e0916eeb4a918b6cb552d4 Tue Oct 8 15:31:21 2019 -0700

• Documenting changes.
  • src/hca/hcat/mysite/versions.txt - lines changed 4, context: html, text, full: html, text

5f2b7d5a6a6942d6676b0a98427ad1b91dbee4c9 Wed Oct 9 15:46:07 2019 -0700

• Adjusting for them turning everything into lists.
  • src/hca/hcat/hcatParseParth/hcatParseParth.c - lines changed 45, context: html, text, full: html, text

97ca263e551d4fada76b8c33ad34e5056fa0e88f Thu Oct 17 19:44:40 2019 -0700

• Adding in handling for landing page (aka index.html).
  • src/hca/hcat/mysite/hcat/admin.py - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/index_urls.py - lines changed 9, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/models.py - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/mysite/hcat/views.py - lines changed 5, context: html, text, full: html, text
  • src/hca/hcat/mysite/mysite/urls.py - lines changed 1, context: html, text, full: html, text
  • src/hca/hcat/mysite/templates/hcat/index.html - lines changed 57, context: html, text, full: html, text

cb844abff2d989553c620ff26c1f0511ed38254d Thu Oct 17 20:06:18 2019 -0700

• Edited down most sections, but beefing up API section.
  • src/hca/hcat/mysite/templates/hcat/index.html - lines changed 11, context: html, text, full: html, text

9618a297ae6763524ac07d192cc60b1cc5667ece Thu Oct 17 23:08:04 2019 -0700

• Finishing documenting API. Replacing HCA logo with a picture of a tuatara and changing formatting a bit.
  • src/hca/hcat/mysite/templates/hcat/index.html - lines changed 8, context: html, text, full: html, text

03c16bfda2fc34d3db89d5c0ec0e03b82323cf86 Thu Oct 17 23:36:07 2019 -0700

• Tweaking formatting a little.
  • src/hca/hcat/mysite/templates/hcat/index.html - lines changed 13, context: html, text, full: html, text

07c2d16f9b66b21fd315c56c7b68a8f8b6e80f28 Fri Oct 18 00:15:55 2019 -0700

• Removing lab affiliation from API. Seems like less is more these days in terms of tracking information on people. There's no clear case for people needing to know.
  • src/hca/hcat/mysite/hcat/api.py - lines changed 7, context: html, text, full: html, text

d5bcf70e2252b482781fce5e87afaef852983354 Fri Oct 18 00:22:31 2019 -0700

• Documenting recent changes
  • src/hca/hcat/mysite/versions.txt - lines changed 8, context: html, text, full: html, text

7c06824caee59a83b81af4fc02bca7705e6263f9 Mon Feb 10 15:30:35 2020 -0800

• Adding new test sets.
  • src/tagStorm/tagStormFromTab/100.divSpec - lines changed 5, context: html, text, full: html, text
  • src/tagStorm/tagStormFromTab/100.tab - lines changed 100, context: html, text, full: html, text
  • src/tagStorm/tagStormFromTab/100.tag - lines changed 517, context: html, text, full: html, text

d13f1c8f1fada76cc569fc0c6f073f76fdeace92 Thu Oct 1 17:03:37 2020 -0700

• We have a shell script that does this so slowly on big files it is painful, so I wrote this in C.
  • src/hg/logCrawl/dbTrackAndSearchUsage/generateUsageStats.py - lines changed 3, context: html, text, full: html, text
  • src/utils/csvToTsv/csvToTsv.c - lines changed 71, context: html, text, full: html, text
  • src/utils/csvToTsv/makefile - lines changed 3, context: html, text, full: html, text

d858704add16d24efbcc1a83ddc110a76a72d857 Sat Oct 3 09:57:23 2020 -0700

• Improving usage statement.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 2, context: html, text, full: html, text

a8287907aff5a8e7b783da53fc9e26a3d2a989a6 Sat Oct 3 09:58:11 2020 -0700

• Improving usage statement.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 1, context: html, text, full: html, text

44221bac6c8204e4f2549139877b9ad42d7e6f0a Sat Oct 3 20:16:09 2020 -0700

• Fixing a bug where you couldn't have a single line use of a defined variable if it's name should match name of output field. Also added first cut of aggregation - count, to be expanded soon.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 83, context: html, text, full: html, text

46cbe5852e09da1ac8f78402722f7cd74229dcb1 Sat Oct 3 22:13:29 2020 -0700

• Adding way to create a field that aggregates unique values.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 104, context: html, text, full: html, text

5d0b7bb9098685d0a547b24328de982f090b9100 Sun Oct 4 09:23:46 2020 -0700

• Adding first cut at stats aggregator
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 38, context: html, text, full: html, text

5deadb92cd2d8ddc11d8e11fee61d5f8faf304d6 Sun Oct 4 09:48:11 2020 -0700

• Made stats output sort so most common occurs first in list.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 28, context: html, text, full: html, text

3cbb4b9933f89be56be960e16e2cce7a94b37ec8 Sun Oct 4 19:29:16 2020 -0700

• Updating test set to include new features of agregating by list
  • src/tabFile/tabToTabDir/tests/expected/donor_organ_cells.tsv - lines changed 13, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/lab_submitters.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/expected/unroll_test.tsv - lines changed 1, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/input/spec.txt - lines changed 15, context: html, text, full: html, text

cfcd633ac84929aca1dca0656cd92e8381a35d68 Sun Oct 4 19:31:49 2020 -0700

• Adding test set for count type field.
  • src/tabFile/tabToTabDir/tests/expected/donor_organ_cells.tsv - lines changed 13, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/input/spec.txt - lines changed 1, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/test.x - lines changed 13, context: html, text, full: html, text

bee3b5304bafb04498dd966ca167a7fbbc9b0e8c Sun Oct 4 19:46:04 2020 -0700

• Adding stats field type to test suite.
  • src/tabFile/tabToTabDir/tests/expected/lab_submitters.tsv - lines changed 2, context: html, text, full: html, text
  • src/tabFile/tabToTabDir/tests/input/spec.txt - lines changed 1, context: html, text, full: html, text

8d70270630439dce0f7b3f5a06d0a2a4f74e395f Tue Oct 6 17:42:17 2020 -0700

• tabToTabDir.doc
  • src/tabFile/tabToTabDir/tabToTabDir.doc - lines changed 91, context: html, text, full: html, text

7e420071260c119b5917eb52a2aa20edf4bc1d94 Tue Oct 6 17:45:55 2020 -0700

• Adding percentage after count in stats output. Moving doc mostly from usage to new tabToTabDir.doc file.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 24, context: html, text, full: html, text

9fc4a45a0bc85ef2d4c397a557fd1d9cd7dee535 Thu Oct 29 11:11:51 2020 -0700

• Documenting 'unroll' stanzas
  • src/tabFile/tabToTabDir/tabToTabDir.doc - lines changed 16, context: html, text, full: html, text

2aa6eaa0d58ff2019e8719decafe720209d421cc Mon Nov 23 11:30:08 2020 -0800

• Making substitution file be tab separated as usage statement says.
  • src/utils/subColumn/subColumn.c - lines changed 21, context: html, text, full: html, text

8d6aa83c01798ccb80e22f049c825369a3320c01 Fri Dec 18 11:24:50 2020 -0800

• First working cut of C program to convert gene expression and similar matrixes to barchart bed files using a 6 or 7 column bed file to describe gene positions.
  • src/utils/clusterMatrixToBarchartBed/clusterMatrixToBarchartBed.c - lines changed 276, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.coords - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.groupOrder - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.matrix - lines changed 11, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.meta - lines changed 8, context: html, text, full: html, text

f6ef041a6fa43e86f7b0c17f79371cb0fdeeaf8f Fri Dec 18 16:28:29 2020 -0800

• Adding utility to help pull out genes positions from a bunch of transcripts and a gene/transcript table.
  • src/hg/txGraph/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/txGraph/txgToGeneBed/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/txGraph/txgToGeneBed/txgToGeneBed.c - lines changed 75, context: html, text, full: html, text

7460f8b77f30387b332655cd1579ced133d9cd03 Fri Dec 18 16:31:46 2020 -0800

• Fixing bug where a trimmed out graph could linger and cause problems.
  • src/hg/txGraph/txBedToGraph/makeGraph.c - lines changed 18, context: html, text, full: html, text
  • src/hg/txGraph/txBedToGraph/txBedToGraph.c - lines changed 1, context: html, text, full: html, text

8b7a946061426398e6c6253e3478dd1ac84450ff Fri Dec 18 16:42:59 2020 -0800

• Adding geneName parameter
  • src/hg/txGraph/txgToGeneBed/txgToGeneBed.c - lines changed 10, context: html, text, full: html, text

21e481b8c5061e91f5e3abd49e92c9bee87be6ca Fri Dec 18 16:56:34 2020 -0800

• A little polishing and adding to parent makefile.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

f0c88ba99715e71d8868232507ddf166270e1e33 Fri Dec 18 18:19:57 2020 -0800

• Allowing a gene name to be multiply mapped.
  • src/utils/clusterMatrixToBarchartBed/clusterMatrixToBarchartBed.c - lines changed 11, context: html, text, full: html, text

b3834f9b6ec64e8b6018eca2c0c737cbd394484c Sat Dec 19 11:24:16 2020 -0800

• Handling some syntax errors with meaningful error messages rather than program crashes.
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 5, context: html, text, full: html, text

4bd8d0793488ed896bf604d1ce7252fd601df161 Sat Dec 19 11:25:30 2020 -0800

• Making hashIncInt return the value (after increment, rather than be void.
  • src/inc/hash.h - lines changed 2, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 7, context: html, text, full: html, text

d1a9d0f8693e766b2214e65c1bcd6942a4718d5a Sat Dec 19 11:28:13 2020 -0800

• Adding a sortStrings function as a little wrapper around qsort for an array of char *'s. Also added microoptimization to doubleSort
  • src/inc/common.h - lines changed 4, context: html, text, full: html, text
  • src/lib/common.c - lines changed 16, context: html, text, full: html, text

80545e15696d2b9c4a6ee26d8a381674af33f0f9 Sat Dec 19 11:30:09 2020 -0800

• Minor doc polish.
  • src/hg/sqlUpdateRelated/sqlUpdateRelated.doc - lines changed 1, context: html, text, full: html, text

114397ec2020824f4cdd0eae3ddce83c86f5c4e7 Sat Dec 19 11:33:09 2020 -0800

• Finally committing this small fix. This should be viewed as one-shot code as it is just a way to pull down data from a server no longer maintained.
  • src/hca/hcat/hcatParseParth/hcatParseParth.c - lines changed 14, context: html, text, full: html, text

b626835f2a7ce78bb6b5b40100d656d225f9f3ca Sat Dec 19 11:33:35 2020 -0800

• Removing debugging message.
  • src/hca/fromGeo/geoToHcaStorm/geoToHcaStorm.c - lines changed 1, context: html, text, full: html, text

fd6d2b2ed29101ad121186dd55d0ef6291d69ccf Sat Dec 19 11:50:31 2020 -0800

• Hoping this isn't a retrograde commit, it's part of a messy merge.

beb03835a67006b093a20746fcaf5b12a7a1156c Sat Dec 19 12:01:02 2020 -0800

• Taking clusterMatrixToBarchartBed out of build chain until I can figure out how to get make clean to work with it in.
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

8135446fb6a4c338e543585aa411808eef36ee10 Sun Dec 20 16:00:10 2020 -0800

• Optimizing speed and polishing comments.
  • src/utils/clusterMatrixToBarchartBed/clusterMatrixToBarchartBed.c - lines changed 45, context: html, text, full: html, text

2d4ce573d9b6e9929d5c2c2481f64bf105b62031 Sun Dec 20 16:06:34 2020 -0800

• Adding making 'clean' rule work and adding to parent makefile again.
  • src/utils/clusterMatrixToBarchartBed/tests/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/makefile - lines changed 1, context: html, text, full: html, text

8bb6956fbfc0b789de4c76938878dd3a4399b3d0 Sun Dec 20 18:09:04 2020 -0800

• Fixing camel casing to be like most of our barChart C code.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarchartBed.c - lines changed 297, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.coords - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.groupOrder - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.matrix - lines changed 11, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.meta - lines changed 8, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/clusterMatrixToBarchartBed.c - lines changed 297, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/makefile - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/makefile - lines changed 7, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.coords - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.groupOrder - lines changed 4, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.matrix - lines changed 11, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarchartBed/tests/test.meta - lines changed 8, context: html, text, full: html, text

47c764d7fd7d2538ccc1d0eacdf19bf0949ab225 Sun Dec 20 18:11:14 2020 -0800

• Fixing camel casing to be like most of our barChart C code.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 297, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarchartBed.c - lines changed 297, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/makefile - lines changed 4, context: html, text, full: html, text

15b999a555451debea863862c67b7b0784cdb20c Sun Dec 20 18:11:46 2020 -0800

• Fixing camel casing to be like most of our barChart C code.
  • src/utils/clusterMatrixToBarChartBed/tests/makefile - lines changed 1, context: html, text, full: html, text

646ff06654a53214f1b47fa6b92742ec6a44934a Mon Dec 21 12:16:42 2020 -0800

• Adding simple barchart display without box plots when no expMatrix available.
  • src/hg/hgc/barChartClick.c - lines changed 56, context: html, text, full: html, text

f8f44ba39e3c8a4c1c92f5332d22d2a3e1f83e2a Tue Dec 22 10:05:53 2020 -0800

• Adding new cases to test set
  • src/utils/clusterMatrixToBarChartBed/tests/makefile - lines changed 5, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/mean.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/median.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/name2.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.expected - lines changed 10, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/test.name2 - lines changed 10, context: html, text, full: html, text

992541b9ac7cdc7f292bc6cc35b8c471e15ffaea Tue Dec 22 10:07:00 2020 -0800

• Adding name2 option. Making mean the default and median a flag.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 55, context: html, text, full: html, text

7538532d26dbee720c6ee3426fab17680d242dd1 Tue Dec 22 11:02:24 2020 -0800

• Estimating width of label based on helvetica font in memory.
  • src/hg/hgc/barChartClick.c - lines changed 21, context: html, text, full: html, text

7a66ec026712b92017d2bf9d2e313ad079eea28f Tue Dec 22 11:04:39 2020 -0800

• Fine tuning some layout constants.
  • src/hg/hgc/barChartClick.c - lines changed 2, context: html, text, full: html, text

9a3b1674fd367695d5ba29e8eab4a60280877bd8 Tue Dec 22 12:32:35 2020 -0800

• Adding label row to expression barchart table.
  • src/hg/hgc/barChartClick.c - lines changed 35, context: html, text, full: html, text

68efbf55fbd3a55194ef24ca5e21d4bb09221c22 Sat Dec 26 13:07:43 2020 -0800

• First version of something to make file to help assign gencode genes and symbols to best transcripts is done.
  • src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c - lines changed 310, context: html, text, full: html, text
  • src/hg/utils/gencodeGeneSymVerTx/makefile - lines changed 3, context: html, text, full: html, text

0787a6e99b0df048ce46baccf261948c5ba10c7a Sat Dec 26 14:45:30 2020 -0800

• Utility to look through ucsc genome directories for best gencode to use.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 225, context: html, text, full: html, text
  • src/hg/utils/gencodeVersionForGenes/makefile - lines changed 3, context: html, text, full: html, text

761fffb81a48ba6ee7596f43a90c9e5069271adc Sat Dec 26 15:07:46 2020 -0800

• Adding ucscDb to output, and making optional bed output include full geneset, not just bits that our particular input matrix uses.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 13, context: html, text, full: html, text

98eab6403a6627259fbbf38b1abc19d2d42387c2 Sat Dec 26 16:09:51 2020 -0800

• Making bed option just give genes we use, and reorder name/name2 to fit data use. Made allBed output to get data dump in Max's cellBrowser gene bed format.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 86, context: html, text, full: html, text

3f2b8e9bd546eadd2883cbd2aecadd998496f334 Sat Dec 26 17:33:37 2020 -0800

• Reducing verbosity and adding percentage missed to output
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 2, context: html, text, full: html, text

0f37bc93a62d4e0b25336becb089f7c42ceef160 Sat Dec 26 17:38:35 2020 -0800

• Reducing verbosity
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 2, context: html, text, full: html, text

45b9bd3fd9a066cb2515629b23c3eef5a10eeb74 Sat Dec 26 20:22:29 2020 -0800

• Making outputting position in expMatrix part of default output.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 6, context: html, text, full: html, text

e41713ca26a553b4fe04ba1e4bc311d92c4e6654 Sun Dec 27 19:11:34 2020 -0800

• Adding a new routine, fieldedTableReadTabHeader, to allow matrix reading code to reuse some of fielded table
  • src/inc/fieldedTable.h - lines changed 8, context: html, text, full: html, text
  • src/lib/fieldedTable.c - lines changed 58, context: html, text, full: html, text

b0118c2f9d714a1913c16443c6684943497509ad Sun Dec 27 21:27:17 2020 -0800

• Adding matrixMarket file routine that helps handle row-at-a-time access in sorted files
  • src/inc/matrixMarket.h - lines changed 47, context: html, text, full: html, text
  • src/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/lib/matrixMarket.c - lines changed 130, context: html, text, full: html, text

7d421618af20105240d24be483214c4259d45601 Mon Dec 28 15:07:59 2020 -0800

• Reordered definition of new function.
  • src/inc/fieldedTable.h - lines changed 13, context: html, text, full: html, text

826d8721b1c1b0a8b1030056c90f14a8d319f5e8 Mon Dec 28 16:30:36 2020 -0800

• First cut of tool designed to cluster big matrices by column. This is a refactoring of clusterMatrixIntoBarchartBed to just handle the matrix shrinking part, whichis the most time consuming and perhaps useful elsewhere.
  • src/utils/matrixClusterColumns/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixClusterColumns/matrixClusterColumns.c - lines changed 420, context: html, text, full: html, text

9186636eb6806a49e2e2cc5fd6b11d690ab729c1 Mon Dec 28 18:36:02 2020 -0800

• A little utility for changing labels in first row and or column of a tsv table.
  • src/utils/matrixRelabel/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixRelabel/matrixRelabel.c - lines changed 121, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.col - lines changed 4, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.in - lines changed 4, context: html, text, full: html, text
  • src/utils/matrixRelabel/test.row - lines changed 3, context: html, text, full: html, text

6aa2022b82fb742c780fec6dc197371c2f299f42 Mon Dec 28 20:49:54 2020 -0800

• Making it so first word is expected to be in the new lables
  • src/utils/matrixRelabel/matrixRelabel.c - lines changed 10, context: html, text, full: html, text

4d18f275081580118e24c54d96caaf93c7963452 Mon Dec 28 20:57:05 2020 -0800

• Updating test set for new command line options setup.
  • src/utils/clusterMatrixToBarChartBed/tests/makefile - lines changed 2, context: html, text, full: html, text
  • src/utils/clusterMatrixToBarChartBed/tests/median.expected - lines changed 10, context: html, text, full: html, text

4602afa7547202518272b4b49c3b188960c538dc Tue Dec 29 10:27:30 2020 -0800

• Making it strip .versions from gencode names if they are stripped in user gene list.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 68, context: html, text, full: html, text

f31aa864d2c8a8bedadffa47cf184f85724ee0d9 Wed Dec 30 15:20:00 2020 -0800

• A little matrix manipulation utility, not very general purpose yet.
  • src/utils/matrixTrim/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixTrim/matrixTrim.c - lines changed 123, context: html, text, full: html, text
  • src/utils/matrixTrim/test.in - lines changed 6, context: html, text, full: html, text

2ec8e153f0b10f84aac7109840f6cab79d5f8902 Wed Dec 30 18:50:13 2020 -0800

• Pastes together matrices in the x-dimension while trimming duplicate row-labels.
  • src/utils/matrixCat/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixCat/matrixPaste.c - lines changed 103, context: html, text, full: html, text
  • src/utils/matrixCat/test.in - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.in2 - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.long - lines changed 9, context: html, text, full: html, text
  • src/utils/matrixCat/test.remix - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.short - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixPaste/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixPaste/matrixPaste.c - lines changed 151, context: html, text, full: html, text
  • src/utils/matrixPaste/test.in - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixPaste/test.in2 - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixPaste/test.long - lines changed 9, context: html, text, full: html, text
  • src/utils/matrixPaste/test.remix - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixPaste/test.short - lines changed 3, context: html, text, full: html, text

e2f20604e7a8eaaa06057a074466ee31c6642adc Thu Dec 31 13:05:18 2020 -0800

• Polishing a little, adding makeIndex option, fixing an off-by-one bug.
  • src/utils/matrixClusterColumns/matrixClusterColumns.c - lines changed 36, context: html, text, full: html, text

a7e2892242a5f79a05b0c2ac6b9230058fc4b97c Thu Dec 31 14:55:36 2020 -0800

• Added lineFileTellSize to get size of current line.
  • src/inc/linefile.h - lines changed 2, context: html, text, full: html, text

9cb00c4f07c40b647094f0d03b2bcce00e535d9c Thu Dec 31 14:56:48 2020 -0800

• Added hashTsvBy since I needed it in two places, and it seems pretty general, but not common.
  • src/inc/obscure.h - lines changed 3, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 28, context: html, text, full: html, text

7b22e08d678f2e36efc345de2dcc850ca8840bcb Thu Dec 31 14:58:29 2020 -0800

• Hopefully getting rid of mixup between gene name and symbol.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 2, context: html, text, full: html, text

901666d674b8e7147670eb2fd3f9e80f0c1d2fbd Thu Dec 31 14:59:45 2020 -0800

• Removed dependency on having less than 16k words/line.
  • src/utils/wordLine/wordLine.c - lines changed 10, context: html, text, full: html, text

b3291f717be7ee6ce33882e0c07cf815d7ac40c5 Thu Dec 31 15:05:10 2020 -0800

• Moved hashTsvBy() to obscure.c. Removed some debugging uglyfs.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 41, context: html, text, full: html, text

a34abddf2f3f018f50f596632a4ba0b1fc6d718b Thu Dec 31 15:06:06 2020 -0800

• Renamed this to matrixPaste
  • src/utils/matrixCat/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixCat/matrixPaste.c - lines changed 103, context: html, text, full: html, text
  • src/utils/matrixCat/test.in - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.in2 - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.long - lines changed 9, context: html, text, full: html, text
  • src/utils/matrixCat/test.remix - lines changed 6, context: html, text, full: html, text
  • src/utils/matrixCat/test.short - lines changed 3, context: html, text, full: html, text

f6a7885f1bd5a869ced47dc1dfed6d03daec7c3a Thu Dec 31 16:15:46 2020 -0800

• Adding median flag and the start of a test set.
  • src/utils/matrixClusterColumns/matrixClusterColumns.c - lines changed 54, context: html, text, full: html, text
  • src/utils/matrixClusterColumns/test.expected - lines changed 11, context: html, text, full: html, text
  • src/utils/matrixClusterColumns/test.matrix - lines changed 11, context: html, text, full: html, text
  • src/utils/matrixClusterColumns/test.meta - lines changed 9, context: html, text, full: html, text

9e970884e47accc964b1fac1e9bd356be9202e84 Thu Dec 31 16:55:22 2020 -0800

• Rearranging command line. Sample is always col0. Added stats output file.
  • src/utils/matrixClusterColumns/matrixClusterColumns.c - lines changed 63, context: html, text, full: html, text

dab44418c480b8c931d0b86af916bbb3bf64ffe3 Fri Jan 1 08:06:26 2021 -0800

• Adding barChartStatsUrl tag. Right now it is ignored by the browser if barChartMatrixUrl is present. It points to a tab separated file with a label row and a few required fields.
  • src/hg/hgc/barChartClick.c - lines changed 33, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 1, context: html, text, full: html, text

6ff0c3e3a83b03257780785c6366ac492a468e9e Fri Jan 1 16:36:46 2021 -0800

• Freen helps me understand how to read strings from heartcellatlas hdf5 files.
  • src/hg/oneShot/freen/freen.c - lines changed 78, context: html, text, full: html, text

0354af7336d81b28d019287703d37be09d32d5c4 Sat Jan 2 19:39:26 2021 -0800

• This made a useful output for the heart cell atlas muscle subset in hdf5 format, converting this file to stuff the cell browser and genome browser understand.
  • src/hca/hcaUnpack5/hcaUnpack5.c - lines changed 699, context: html, text, full: html, text
  • src/hca/hcaUnpack5/makefile - lines changed 4, context: html, text, full: html, text

4e97a66a0e7013279c1726f581fdd5dab079a023 Sat Jan 2 19:41:33 2021 -0800

• Some experiments with hdf5 files from heartcellatlas.org
  • src/hg/oneShot/freen/freen.c - lines changed 10, context: html, text, full: html, text
  • src/hg/oneShot/freen/makefile - lines changed 1, context: html, text, full: html, text

26bdb2dad348ff9eae2a6846b4af6458a8893328 Sat Jan 2 21:16:12 2021 -0800

• Another little matrix utility.
  • src/utils/matrixScale/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixScale/matrixScale.c - lines changed 76, context: html, text, full: html, text

76bba8a5c8a2b584ac5cd9d0610395c0617cf7e6 Sun Jan 3 14:04:57 2021 -0800

• Program for attaching a barchart track to a matrix with option to make a trackDb stanza.
  • src/utils/matrixToBarChartBed/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixToBarChartBed/matrixClusterStats.as - lines changed 7, context: html, text, full: html, text
  • src/utils/matrixToBarChartBed/matrixToBarChartBed.c - lines changed 262, context: html, text, full: html, text