File Changes for kent

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

• src/hca/LICENSE
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    49f37c9142eb832f5fe91d7586c7f8a0c1216953 Mon Jan 11 12:58:50 2021 -0800
    Updating copyright date to include 2021
• src/hca/hcaColorCells/hcaColorCells.c
  • lines changed 332, 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.
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    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.
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    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/makefile
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    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/hcaUnpack5/hcaUnpack5.c
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    42fbe7842ac08e964f712072b62724f7dec7e89c Mon Jan 4 17:36:09 2021 -0800
    Refactoring in prep for moving sparseRowMatrix stuff to library
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    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.
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    47f8a20771d50c3b3c24d525dee1df764be3fe1f Mon Jan 11 13:02:51 2021 -0800
    Updating usage statement
• src/hg/hgTracks/barChartTrack.c
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    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/hgc/barChartClick.c
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    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/inc/barChartUi.h
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    3d1baa9a169fe449fc22aa04eaf02a3ae137781d Mon Jan 11 15:01:03 2021 -0800
    Making transformFunc apply to barCharts. Adding barChartLimit.
• src/hg/inc/trackDb.h
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    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/lib/barChartUi.c
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    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.
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    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/simpleBarChartBed.as
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    5c53721cad04423b6081f27b315b0d584807a0ea Wed Jan 6 16:04:43 2021 -0800
    Added a barChart with fewer fields because I don't have and index for exprMatrix.
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    cf897e4aa00e43dd707f6f2b1aa79020bc804445 Mon Jan 11 14:38:30 2021 -0800
    Shortening a description.
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    43436c471e8e0c1fc922f45e10b8e8e079f0a59d Tue Jan 12 11:09:23 2021 -0800
    Changing table name
• src/hg/lib/trackDbCustom.c
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    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/lib/trackHub.c
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    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/makeDb/hgTrackDb/hgTrackDb.c
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    58082337569fd56e1150c52f0a55955ee42e71c5 Mon Jan 11 14:43:34 2021 -0800
    Making getBarChartStatsUrl get variable substituted.
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    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/makeDb/trackDb/human/hg19/fetalGeneAtlas.ra
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    c000f4b75359c1bad9b84c793cdfbfab60e3ec97 Sun Jan 10 18:36:30 2021 -0800
    Adding fetalGeneAtlas to hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
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    c000f4b75359c1bad9b84c793cdfbfab60e3ec97 Sun Jan 10 18:36:30 2021 -0800
    Adding fetalGeneAtlas to hg19
• src/hg/makeDb/trackDb/human/hg38/bloodHao.ra
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    c3a3b7e3f381352124fc44a196fc94989edc91be Mon Jan 11 14:42:21 2021 -0800
    Being consistent about using 'binned by' rather than 'sorted by'
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    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/cortexVelmeshev.ra
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    003cc83285b42feb62f816b43ad2c129e9bbaf36 Sat Jan 9 15:58:47 2021 -0800
    Adding cortexVelmeshev and heartCellAtlas supertracks
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    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/fetalGeneAtlas.ra
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    9a068535365abc9308bc15ca4b3e3ab2b75cc6a9 Sun Jan 10 19:21:20 2021 -0800
    Adding fetalGeneAtlas lifted version to hg38
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    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/heartCellAtlas.ra
  • lines changed 191, context: html, text, full: html, text
    003cc83285b42feb62f816b43ad2c129e9bbaf36 Sat Jan 9 15:58:47 2021 -0800
    Adding cortexVelmeshev and heartCellAtlas supertracks
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    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/kidneyStewart.ra
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    38e5f2ae882777653eb496e91c47b8702e1fc9fa Sat Jan 9 20:39:00 2021 -0800
    Adding kidneyStewart single cell supertrack.
• src/hg/makeDb/trackDb/human/hg38/lungVieiraBraga.ra
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    029e421b5aa5d01f1b0bb131b2bbd8b44333fecd Sun Jan 10 11:55:19 2021 -0800
    Adding lungVieiraBraga data set from Teichman lab.
• src/hg/makeDb/trackDb/human/hg38/muscleDeMicheli.ra
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    08591f8a1f2eb71b2706af96e8649412cfd6950a Sat Jan 9 22:15:15 2021 -0800
    Adding muscleDeMicheli single cell data set.
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    003cc83285b42feb62f816b43ad2c129e9bbaf36 Sat Jan 9 15:58:47 2021 -0800
    Adding cortexVelmeshev and heartCellAtlas supertracks
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    38e5f2ae882777653eb496e91c47b8702e1fc9fa Sat Jan 9 20:39:00 2021 -0800
    Adding kidneyStewart single cell supertrack.
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    08591f8a1f2eb71b2706af96e8649412cfd6950a Sat Jan 9 22:15:15 2021 -0800
    Adding muscleDeMicheli single cell data set.
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    029e421b5aa5d01f1b0bb131b2bbd8b44333fecd Sun Jan 10 11:55:19 2021 -0800
    Adding lungVieiraBraga data set from Teichman lab.
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    9a068535365abc9308bc15ca4b3e3ab2b75cc6a9 Sun Jan 10 19:21:20 2021 -0800
    Adding fetalGeneAtlas lifted version to hg38
• src/hg/makeDb/trackDb/tagTypes.tab
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    f9ff87e94780b2e5a4c74df653e16a28b976f0d8 Mon Jan 11 14:39:22 2021 -0800
    Making transformFunc apply to barCharts. Adding barChartLimit.
• src/hg/oneShot/freen/freen.c
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    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.
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    138a38b35d9c7a79f991ad12c4a993b6eb160352 Tue Jan 5 19:40:30 2021 -0800
    The first version worth using. I should give it a name!
• src/hg/oneShot/freen/makefile
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    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/txGraph/makefile
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    315ac2b4d26b6ef65d4ff1fcd822f849153790cb Tue Jan 12 12:49:38 2021 -0800
    Oops, forgot to take utility I deleted out of makefile.
• src/hg/txGraph/txgToGeneBed/makefile
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    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/txgToGeneBed.c
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    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/utils/gencodeGeneSymVerTx/gencodeGeneSymVerTx.c
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    09696c13b5115e7e36104c0f94ab0cbe5e099b5d Tue Jan 12 11:11:57 2021 -0800
    Improving usage message upon code review advice.
• src/hg/utils/gencodeVersionForGenes/gencodeVersionForGenes.c
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    d7636b6985ad8f40784e87854b9e2c383c1ca4b3 Mon Jan 11 14:48:06 2021 -0800
    Adding geneToId output option.
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    7ad18256b4d7adadd102d15ffa70f5c628cc29ff Mon Jan 11 16:00:12 2021 -0800
    Improving usage statement about where the reference file is kept.
• src/inc/cheapcgi.h
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    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/obscure.h
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    946ec4deb61682f1608c3c8f08dfd1ed838fc6d6 Mon Jan 11 14:56:33 2021 -0800
    Added a basic tab-sep output a line to library.
• src/inc/sparseMatrix.h
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    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/inc/vMatrix.h
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    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.
  • lines changed 4, 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/lib/cheapcgi.c
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    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/lib/makefile
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    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/lib/obscure.c
  • lines changed 13, 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/lib/sparseMatrix.c
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    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.
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    99da3db1b62d39f9ed0e24c5fb65ba3392e575dd Mon Jan 11 14:57:13 2021 -0800
    Moving writeTsvRow to lib/obscure.c
• src/lib/strex.c
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    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/vMatrix.c
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    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.
  • lines changed 9, 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/tabFile/tabToTabDir/tabToTabDir.c
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    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/utils/clusterMatrixToBarChartBed/clusterMatrixToBarChartBed.c
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    ee6a0d80b7fc2cf0cac37157b36834ef39a32c33 Sat Jan 9 09:20:30 2021 -0800
    Adding note about other utilities that do similar things to usage statement.
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    b09810165e57a61fc8e61549ea87da8b2dca3f58 Mon Jan 11 15:50:41 2021 -0800
    Changing some Barchart to BarChart that I'd missed.
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    b640e1cf96ee2c383dbf464c1737786945497fcb Mon Jan 11 15:51:38 2021 -0800
    Removing debugging statement.
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    482d460b09a00806e44c9df3005fad97ce173ec1 Tue Jan 12 11:13:48 2021 -0800
    Fixing an off by one bug Jonathan spotted during code review.
• src/utils/matrixNormalize/makefile
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/matrixNormalize.c
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/tests/colLength.out
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/tests/colSum.out
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/tests/rowLength.out
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/tests/rowSum.out
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixNormalize/tests/test.in
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    2e56b90285da462507a48babb2f9aee32dcbb96c Sat Jan 9 11:08:01 2021 -0800
    A little matrix normalizing command, one of many in the world.
• src/utils/matrixRelabel/matrixRelabel.c
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    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/matrixScale/matrixScale.c
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    6f5ac0886db21eaeb6d4d158c85bbf60527761e1 Mon Jan 11 18:07:07 2021 -0800
    Fixed usage statement per code review #26745
• src/utils/matrixToBarChartBed/matrixToBarChartBed.c
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    9a51fe6723423851ee77535b465399a52e244084 Mon Jan 11 18:16:04 2021 -0800
    Improving usage statement per code review #26745