Commits for kent

v409_preview2 to v409_base (2021-01-11 to 2021-01-18) v409

42fbe7842ac08e964f712072b62724f7dec7e89c Mon Jan 4 17:36:09 2021 -0800

• Refactoring in prep for moving sparseRowMatrix stuff to library
  • src/hca/hcaUnpack5/hcaUnpack5.c - lines changed 81, context: html, text, full: html, text

a3939547c53f1ccb39910e61bfa90a0c54310273 Tue Jan 5 00:40:36 2021 -0800

• First cut of vRowMatrix to stream through a variety of matrices semi-transparently I hope. FOr now just handles tsv though.
  • src/hca/hcaUnpack5/hcaUnpack5.c - lines changed 109, context: html, text, full: html, text
  • src/inc/sparseMatrix.h - lines changed 40, context: html, text, full: html, text
  • src/inc/vMatrix.h - lines changed 64, context: html, text, full: html, text
  • src/lib/makefile - lines changed 2, context: html, text, full: html, text
  • src/lib/sparseMatrix.c - lines changed 100, context: html, text, full: html, text
  • src/lib/vMatrix.c - lines changed 254, context: html, text, full: html, text

5f443dee868d091ae2523a1b6f9b4e6ddc90b3d0 Tue Jan 5 15:37:01 2021 -0800

• Freen plays with colors for new single cell RNA tracks, and generates many shades of mostly brown.
  • src/hg/oneShot/freen/freen.c - lines changed 187, context: html, text, full: html, text

138a38b35d9c7a79f991ad12c4a993b6eb160352 Tue Jan 5 19:40:30 2021 -0800

• The first version worth using. I should give it a name!
  • src/hg/oneShot/freen/freen.c - lines changed 29, context: html, text, full: html, text

4bce1472593c4e9966e54e5cf3e44dd30930a252 Tue Jan 5 23:34:51 2021 -0800

• This code that colors based on labeling some but not all of the set and dimming out the samples that are too small, is working in an ad-hoc but good for the moment way.
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 332, context: html, text, full: html, text
  • src/hca/hcaColorCells/makefile - lines changed 3, context: html, text, full: html, text

5c53721cad04423b6081f27b315b0d584807a0ea Wed Jan 6 16:04:43 2021 -0800

• Added a barChart with fewer fields because I don't have and index for exprMatrix.
  • src/hg/lib/simpleBarChartBed.as - lines changed 13, context: html, text, full: html, text

64dbe134613f4d0846e314bf4d4249814f0ea3e3 Wed Jan 6 22:09:24 2021 -0800

• Removed a loop that could be folded into it's neighbor in part so could debug easier.
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 7, context: html, text, full: html, text

ee6a0d80b7fc2cf0cac37157b36834ef39a32c33 Sat Jan 9 09:20:30 2021 -0800

• Adding note about other utilities that do similar things to usage statement.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 1, context: html, text, full: html, text

2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800

• A little matrix normalizing command, one of many in the world.
  • src/utils/matrixNormalize/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/matrixNormalize/matrixNormalize.c - lines changed 174, context: html, text, full: html, text
  • src/utils/matrixNormalize/tests/colLength.out - lines changed 5, context: html, text, full: html, text
  • src/utils/matrixNormalize/tests/colSum.out - lines changed 5, context: html, text, full: html, text
  • src/utils/matrixNormalize/tests/rowLength.out - lines changed 4, context: html, text, full: html, text
  • src/utils/matrixNormalize/tests/rowSum.out - lines changed 4, context: html, text, full: html, text
  • src/utils/matrixNormalize/tests/test.in - lines changed 5, context: html, text, full: html, text

003cc83285b42feb62f816b43ad2c129e9bbaf36 Sat Jan 9 15:58:47 2021 -0800

• Adding cortexVelmeshev and heartCellAtlas supertracks
  • src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra - lines changed 100, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra - lines changed 191, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 3, context: html, text, full: html, text

38e5f2ae882777653eb496e91c47b8702e1fc9fa Sat Jan 9 20:39:00 2021 -0800

• Adding kidneyStewart single cell supertrack.
  • src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra - lines changed 100, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

08591f8a1f2eb71b2706af96e8649412cfd6950a Sat Jan 9 22:15:15 2021 -0800

• Adding muscleDeMicheli single cell data set.
  • src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra - lines changed 45, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

029e421b5aa5d01f1b0bb131b2bbd8b44333fecd Sun Jan 10 11:55:19 2021 -0800

• Adding lungVieiraBraga data set from Teichman lab.
  • src/hg/makeDb/trackDb/human/hg38/lungVieiraBraga.ra - lines changed 25, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 1, context: html, text, full: html, text

c000f4b75359c1bad9b84c793cdfbfab60e3ec97 Sun Jan 10 18:36:30 2021 -0800

• Adding fetalGeneAtlas to hg19
  • src/hg/makeDb/trackDb/human/hg19/fetalGeneAtlas.ra - lines changed 150, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.ra - lines changed 2, context: html, text, full: html, text

9a068535365abc9308bc15ca4b3e3ab2b75cc6a9 Sun Jan 10 19:21:20 2021 -0800

• Adding fetalGeneAtlas lifted version to hg38
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 151, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 2, context: html, text, full: html, text

ea1646068170b191834889377e21b1bd51259175 Mon Jan 11 12:56:25 2021 -0800

• Putting this under control of svgBarChart variable in hg.conf to keep feature from leaking to users too soon. Changing N column display of numbers to be right justified as numbers usually are. Looking up with names in stats table with and without underbars..
  • src/hg/hgc/barChartClick.c - lines changed 12, context: html, text, full: html, text

49f37c9142eb832f5fe91d7586c7f8a0c1216953 Mon Jan 11 12:58:50 2021 -0800

• Updating copyright date to include 2021
  • src/hca/LICENSE - lines changed 1, context: html, text, full: html, text

a4a8aa46f4f60a4be71130450a0c1df2d696dd51 Mon Jan 11 13:00:40 2021 -0800

• Making this slightly better about unhexing gracefully. Arguably should put the new unpackHexString function in the hex.c/h library since hexToByte will do weird things on bad input.
  • src/hca/hcaColorCells/hcaColorCells.c - lines changed 38, context: html, text, full: html, text

47f8a20771d50c3b3c24d525dee1df764be3fe1f Mon Jan 11 13:02:51 2021 -0800

• Updating usage statement
  • src/hca/hcaUnpack5/hcaUnpack5.c - lines changed 1, context: html, text, full: html, text

05620087b2039bbaa6adbad11eabc6276df45840 Mon Jan 11 13:57:15 2021 -0800

• Changing barChart's maxViewLimit to be a floating point rather than an integer. Making logTransform have a default that can be set in trackDb.
  • src/hg/hgTracks/barChartTrack.c - lines changed 4, context: html, text, full: html, text

a1e57595bda0dc8a20c2548f47a4874ebe29e37b Mon Jan 11 14:37:05 2021 -0800

• Making log-transformable for barCharts be settable via transformFunc trackDb setting. Factoring out barChartCurViewMax for reuse elsewhere.
  • src/hg/lib/barChartUi.c - lines changed 29, context: html, text, full: html, text

cf897e4aa00e43dd707f6f2b1aa79020bc804445 Mon Jan 11 14:38:30 2021 -0800

• Shortening a description.
  • src/hg/lib/simpleBarChartBed.as - lines changed 1, context: html, text, full: html, text

f9ff87e94780b2e5a4c74df653e16a28b976f0d8 Mon Jan 11 14:39:22 2021 -0800

• Making transformFunc apply to barCharts. Adding barChartLimit.
  • src/hg/makeDb/trackDb/tagTypes.tab - lines changed 2, context: html, text, full: html, text

c3a3b7e3f381352124fc44a196fc94989edc91be Mon Jan 11 14:42:21 2021 -0800

• Being consistent about using 'binned by' rather than 'sorted by'
  • src/hg/makeDb/trackDb/human/hg38/bloodHao.ra - lines changed 128, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/cortexVelmeshev.ra - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/fetalGeneAtlas.ra - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/heartCellAtlas.ra - lines changed 12, context: html, text, full: html, text

58082337569fd56e1150c52f0a55955ee42e71c5 Mon Jan 11 14:43:34 2021 -0800

• Making getBarChartStatsUrl get variable substituted.
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 1, context: html, text, full: html, text

118dd60772dacb0ee6e8612f31a702fe2b6e7ebf Mon Jan 11 14:45:03 2021 -0800

• Taking special -lhdf5 line out of link libraries since freen no longer needs them.
  • src/hg/oneShot/freen/makefile - lines changed 1, context: html, text, full: html, text

d7636b6985ad8f40784e87854b9e2c383c1ca4b3 Mon Jan 11 14:48:06 2021 -0800

• Adding geneToId output option.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 21, context: html, text, full: html, text

ff2840f7c732b4d9d368ce18ddcac2ce6c7148ee Mon Jan 11 14:50:23 2021 -0800

• Adding options to do table lookup on labels, to trim them, and renaming some old options to be more clear.
  • src/utils/matrixRelabel/matrixRelabel.c - lines changed 57, context: html, text, full: html, text

067cd6631ecf656cbe692e31ed033bc916979bf5 Mon Jan 11 14:55:21 2021 -0800

• Adding in cgiMakeDoublVarWithExtra so as to be able to disable a double countrol the same way you do an int one.
  • src/inc/cheapcgi.h - lines changed 2, context: html, text, full: html, text
  • src/lib/cheapcgi.c - lines changed 8, context: html, text, full: html, text

946ec4deb61682f1608c3c8f08dfd1ed838fc6d6 Mon Jan 11 14:56:33 2021 -0800

• Added a basic tab-sep output a line to library.
  • src/inc/obscure.h - lines changed 3, context: html, text, full: html, text
  • src/lib/obscure.c - lines changed 13, context: html, text, full: html, text

99da3db1b62d39f9ed0e24c5fb65ba3392e575dd Mon Jan 11 14:57:13 2021 -0800

• Moving writeTsvRow to lib/obscure.c
  • src/lib/sparseMatrix.c - lines changed 14, context: html, text, full: html, text

f1eb91ba57a988ea0919c1ecebc45d3f926fc6c1 Mon Jan 11 14:58:50 2021 -0800

• Adding 'centerLabel' to data structure. In TSV representation this is the first word in the file, in the upper left, where it could be constued to label first column or first row.
  • src/inc/vMatrix.h - lines changed 4, context: html, text, full: html, text
  • src/lib/vMatrix.c - lines changed 9, context: html, text, full: html, text

3d1baa9a169fe449fc22aa04eaf02a3ae137781d Mon Jan 11 15:01:03 2021 -0800

• Making transformFunc apply to barCharts. Adding barChartLimit.
  • src/hg/inc/barChartUi.h - lines changed 8, context: html, text, full: html, text

b09810165e57a61fc8e61549ea87da8b2dca3f58 Mon Jan 11 15:50:41 2021 -0800

• Changing some Barchart to BarChart that I'd missed.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 7, context: html, text, full: html, text

b640e1cf96ee2c383dbf464c1737786945497fcb Mon Jan 11 15:51:38 2021 -0800

• Removing debugging statement.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 4, context: html, text, full: html, text

cf64dcdf6ac6c74bb60f4fd2d58c155d0c6ba32b Mon Jan 11 15:54:57 2021 -0800

• Did not need this experimental utility after all, there was a better way with appris database.
  • src/hg/txGraph/txgToGeneBed/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/txGraph/txgToGeneBed/txgToGeneBed.c - lines changed 80, context: html, text, full: html, text

7ad18256b4d7adadd102d15ffa70f5c628cc29ff Mon Jan 11 16:00:12 2021 -0800

• Improving usage statement about where the reference file is kept.
  • src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c - lines changed 3, context: html, text, full: html, text

3b8231d6039e2a9ffc012414a7881ebf72eee458 Mon Jan 11 16:50:51 2021 -0800

• Implementing subtraction, since it was in the docs, as Jonathon pointed out. #ref 26745
  • src/lib/strex.c - lines changed 41, context: html, text, full: html, text

dcc1ce202a76ae34567a597feebb216f390e3bb0 Mon Jan 11 18:05:57 2021 -0800

• Improved usage and explicitly fv->type - good ideas from Jonathan's code review ref #26745
  • src/tabFile/tabToTabDir/tabToTabDir.c - lines changed 3, context: html, text, full: html, text

6f5ac0886db21eaeb6d4d158c85bbf60527761e1 Mon Jan 11 18:07:07 2021 -0800

• Fixed usage statement per code review #26745
  • src/utils/matrixScale/matrixScale.c - lines changed 1, context: html, text, full: html, text

9a51fe6723423851ee77535b465399a52e244084 Mon Jan 11 18:16:04 2021 -0800

• Improving usage statement per code review #26745
  • src/utils/matrixToBarChartBed/matrixToBarChartBed.c - lines changed 3, context: html, text, full: html, text

43436c471e8e0c1fc922f45e10b8e8e079f0a59d Tue Jan 12 11:09:23 2021 -0800

• Changing table name
  • src/hg/lib/simpleBarChartBed.as - lines changed 1, context: html, text, full: html, text

09696c13b5115e7e36104c0f94ab0cbe5e099b5d Tue Jan 12 11:11:57 2021 -0800

• Improving usage message upon code review advice.
  • src/hg/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c - lines changed 2, context: html, text, full: html, text

482d460b09a00806e44c9df3005fad97ce173ec1 Tue Jan 12 11:13:48 2021 -0800

• Fixing an off by one bug Jonathan spotted during code review.
  • src/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c - lines changed 1, context: html, text, full: html, text

315ac2b4d26b6ef65d4ff1fcd822f849153790cb Tue Jan 12 12:49:38 2021 -0800

• Oops, forgot to take utility I deleted out of makefile.
  • src/hg/txGraph/makefile - lines changed 1, context: html, text, full: html, text

82f289a4ffc0110281bed73bd64319201d4fca38 Tue Jan 12 18:01:09 2021 -0800

• Slight tweaking of red colors. Better labeling of one track. Experimenting with Kate's barChartCategoryUrl. Careful hgTracks crashes if there is a barChartCategoryUrl that points to a nonexistent file.
  • src/hg/makeDb/trackDb/human/hg38/bloodHao.ra - lines changed 9, context: html, text, full: html, text

2c8912b056f0460badfcad9cce2e5c0a8c290c6d Tue Jan 12 18:06:55 2021 -0800

• Refactoring code so that in both hubs and in built in tracks the same trackDb fields are D substituted for file names so they don't have to be maintained in parallel. Build a new trackSettingIsFile routine to enable this and am calling it in the two places that used to decide whether to do a substitution.
  • src/hg/inc/trackDb.h - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/trackDbCustom.c - lines changed 12, context: html, text, full: html, text
  • src/hg/lib/trackHub.c - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/hgTrackDb/hgTrackDb.c - lines changed 6, context: html, text, full: html, text

e302bb6915d4003f97dacfa9637e78dc0fb98303 Tue Jan 12 18:44:00 2021 -0800

• Fixing logic error I recently introduced. The checkbox by the log-transform on barCharts should behave better now.
  • src/hg/lib/barChartUi.c - lines changed 6, context: html, text, full: html, text