All File Changes

v410_preview to v410_preview2 (2021-01-25 to 2021-02-01) v410

• confs/asia.hg.conf
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    1d4b5d5471a54015d8915f4b62edeaabf3994ce8 Sun Jan 31 01:12:00 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/euro.hg.conf
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    1d4b5d5471a54015d8915f4b62edeaabf3994ce8 Sun Jan 31 01:12:00 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/hgwbeta.hg.conf
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    1d4b5d5471a54015d8915f4b62edeaabf3994ce8 Sun Jan 31 01:12:00 2021 -0800
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
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    1d4b5d5471a54015d8915f4b62edeaabf3994ce8 Sun Jan 31 01:12:00 2021 -0800
    Installing updated hg.conf files from UCSC servers
• src/hg/hgPhyloPlace/phyloPlace.c
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    0f5e8ee9ef8d65cf207610e97d1ce7c368623df5 Wed Jan 27 15:13:20 2021 -0800
    qBaseInsert and tBaseInsert may include sequence skipped on both sides, e.g. due to NNN's. Count actual inserted and deleted bases more carefully. refs #26868
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    6c08bf0d066841b266c00d1da5e5be5652cde7c8 Thu Jan 28 14:49:34 2021 -0800
    Now that the correct numbers of inserted and deleted bases are reported, make the tooltips more helpful by reporting the bases and locations. sorta refs #26868
• src/hg/hgPhyloPlace/runUsher.c
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    f03ed98b4b88609222f264bd1bed65f3b3bab9c9 Tue Jan 26 16:57:47 2021 -0800
    Don't crash if usher omits internal node labels in subtree Newick file. Case found by Russ (subtree size = 500).
• src/hg/hgTrackUi/hgTrackUi.c
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/hgTracks/bigBedTrack.c
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/hgTracks/simpleTracks.c
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/hgc/hgc.c
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    31f6f53e9ec2946db4073667fe6e73948375c773 Fri Jan 29 09:30:53 2021 -0800
    back out a change that was causing hgGene to not support getting sequence if it's a gene track that uses bigGeneDataUrl
• src/hg/htdocs/cite.html
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    bfc920a91a9dc0a179a4bdb0e89f198496460913 Fri Jan 29 15:22:41 2021 -0800
    Typo fix and replacing hgsid note with session note refs #26860
• src/hg/htdocs/goldenPath/credits.html
  • lines changed 6, context: html, text, full: html, text
    a02e1b9169c21c900761170e54a6ffb42597da68 Mon Jan 25 13:41:07 2021 -0800
    Adding new assembly canFam5 to credits.html #25917
• src/hg/htdocs/goldenPath/help/mysql.html
  • lines changed 3, context: html, text, full: html, text
    ec718fd2194d00986a11c213886e6a584d1c00b9 Wed Jan 27 11:51:52 2021 -0800
    Adding a link to the conditions.html page on the MYSQL help page, no Redmine.
• src/hg/htdocs/goldenPath/history.html
  • lines changed 2, context: html, text, full: html, text
    0214da4a034d28253fffea4589e25600c5505348 Tue Jan 26 16:02:30 2021 -0800
    Adding a link to the Single Cell Browser as per Jim's request, refs #20314
• src/hg/htdocs/goldenPath/newsarch.html
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    c8aa03601d740d2dd2d44d373d6513e0712344f5 Mon Jan 25 13:58:52 2021 -0800
    Adding new assembly canFam5 to newsArch page #25917
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    0c12430b872310f016b018db863d09697dc4deaf Tue Jan 26 11:49:25 2021 -0800
    Code review edits to gnomAD track announcement, updated CGI links, and uncapitalized words, refs #26858
• src/hg/htdocs/goldenPath/pubs.html
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    83e6c0e62129cd2a0f91ea531ecf9ecf19d1c11f Wed Jan 27 11:49:32 2021 -0800
    Adding the latest Genome Browser NAR paper to the publications list, no Redmine.
• src/hg/htdocs/indexNews.html
  • lines changed 12, context: html, text, full: html, text
    fa29482ccf7e2ac9568be54cc212df3fc8a02e81 Mon Jan 25 14:01:39 2021 -0800
    Adding new assembly canFam5 to indexNews page #25917
• src/hg/htdocs/staff.html
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    63f5014fc0a9d0b1b339f4f691884c0f8025062d Mon Mar 23 15:30:53 2020 -0700
    Updaging Parisa Nejad and Clay Fischer's roles.
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    ff7a34e88550b3c8cd5af5708de75e2460256c6c Thu Oct 29 10:47:22 2020 -0700
    Adding Rachel and Brittney to the Staff page.
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    445b99ac04a01acd28e484a919e8d9893ecd4046 Wed Jan 27 14:35:39 2021 -0800
    Adding Rachel and Brittney to the staff page.
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    df9b8dc8ccf72d3a3c10c5e4f3bda7962343c8bf Wed Jan 27 14:51:43 2021 -0800
    Updated Will, Brittney pointed out we need to also update the year and group photo.
• src/hg/js/hgTracks.js
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    8e1d11e9de8d0b27b4d31169e7cf2994d3821533 Mon Jan 25 13:43:14 2021 -0800
    correctly measuring size of text for popUp sizing refs #21980
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    b0edcec43a680887f447440764d2c6479b5f8c1b Tue Jan 26 09:05:19 2021 -0800
    change mu to ~ refs #21980
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    1256e2de30fbb9edd29e824471519cda5c016ffe Tue Jan 26 11:23:25 2021 -0800
    try placing the message box at the bottom of the track when it is scrolled off the top refs #21980
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    6de82671728ebf25c3edff3c677fc291d72a96c5 Tue Jan 26 15:39:25 2021 -0800
    turn off popUp when track scrolls off top refs #21980
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    4178628e88ad4af932683334ef34430a7bfbef3d Tue Jan 26 21:09:05 2021 -0800
    avoid cursor covering popUp message box refs #21980
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    82a65b272b0d71896100ce9e8613abb07b781f25 Wed Jan 27 12:19:46 2021 -0800
    no need to switch to bottom of track, just pin at the top of the window refs #21980
• src/hg/lib/hui.c
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/lib/wiggleCart.c
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    cbfd2211326099053c026e0cf592c130d1a1905b Wed Jan 27 15:28:53 2021 -0800
    Revert "As for wiggle, make bigWig's viewLimits min and max come from the data." refs #26872 This reverts commit 9a1dd73f2df69278e2b5ab8c62d531205ab87845.
• src/hg/makeDb/doc/asmHubs/asmHubs.mk
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    ec576d8762ce7994a38c6adeac8920e6d4d8cddf Mon Jan 25 16:21:14 2021 -0800
    add the hub index pages to the sendDownload push rule refs #23891
• src/hg/makeDb/doc/asmHubs/mkGenomes.pl
  • lines changed 3, context: html, text, full: html, text
    2bcf12483a026f2f164ad1748334d0dec72a26de Mon Jan 25 15:21:25 2021 -0800
    can use better common name when available for genomes.txt description refs #23891
• src/hg/makeDb/doc/mammalsAsmHub/mammals.orderList.tsv
  • lines changed 15, context: html, text, full: html, text
    6758381a8bc781f9ffe3f806385c1d0239c6b92a Mon Jan 25 15:22:45 2021 -0800
    update some common names to make them unique refs #23891
• src/hg/makeDb/doc/primatesAsmHub/primates.orderList.tsv
  • lines changed 2, context: html, text, full: html, text
    e0e3fe06a929d36585cc38f7e6c332969979b882 Mon Jan 25 15:51:39 2021 -0800
    update some common names to make them unique refs #23891
• src/hg/makeDb/doc/ucscGenes/hg38.gencodeV36.sh
  • lines changed 136, context: html, text, full: html, text
    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/makeDb/schema/all.joiner
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    618a2c33906032a84cc43cc9d975156525228535 Thu Jan 28 15:15:37 2021 -0800
    Added all.joiner for GTEx V8. refs #26885
• src/hg/makeDb/trackDb/human/cadd.ra
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    e5e64c5bf85b5a4fcc79bd7264e9ae7145973104 Thu Jan 28 08:47:55 2021 -0800
    fixing mouseover for CADD, refs #18492
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.html
  • lines changed 66, context: html, text, full: html, text
    05aabb8581b9175ce0511324bb158456d1b2b7ca Thu Jan 28 09:15:30 2021 -0800
    plug in the right html from knownGene alpha
• src/hg/makeDb/trackDb/human/hg38/knownGene.alpha.ra
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
  • lines changed 1, context: html, text, full: html, text
    05aabb8581b9175ce0511324bb158456d1b2b7ca Thu Jan 28 09:15:30 2021 -0800
    plug in the right html from knownGene alpha
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/makeDb/trackDb/human/trackDb.ra
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    0fd06e84a62da69e089e6b6f3b7d39c2e9f1f80b Tue Jan 26 07:03:52 2021 -0800
    making lovd track label more specific, email from Ana, thread with chris and lou, no redmine
• src/hg/makeDb/trackDb/makefile
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    7528b6b68b9162fb9c69b2ffb43fde8eea9e3a35 Thu Jan 28 17:51:12 2021 -0800
    check the RR or beta for the presence of bigDataUrl referenced files before adding them to trackDb.
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    0bf35fe45f0e6dd61969f84fdf301348e3a9ec5f Fri Jan 29 07:45:39 2021 -0800
    oops... left a Test in where there shouldn't be one
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    f0f0e9189da0e57ce9d327d9ac8720ae01570bdc Fri Jan 29 14:48:21 2021 -0800
    ignore errors from find when making beta or public
• src/hg/makeDb/trackDb/mouse/mm39/cons35way.html
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    921b06ec6406fe1d2a3c9c6bdaa8dd6db184af21 Tue Jan 26 17:20:04 2021 -0800
    Data access, pennantIcon, default species changes for mm39 cons track refs #26584
• src/hg/makeDb/trackDb/mouse/mm39/trackDb.35way.ra
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    921b06ec6406fe1d2a3c9c6bdaa8dd6db184af21 Tue Jan 26 17:20:04 2021 -0800
    Data access, pennantIcon, default species changes for mm39 cons track refs #26584
• src/hg/makeDb/trackDb/tagTypes.tab
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    9c6055fba90d52e081a16fa54bd3a2b31a7243a6 Wed Jan 27 16:30:13 2021 -0800
    changing back to the old knownGene model
• src/hg/makeDb/trackDb/trackDb.uniprot.ra
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    e6a2e01522e05ba2f2db2b5da7e33f8bcc5a955d Fri Jan 29 09:17:22 2021 -0800
    adding uniprot interest track, refs #26889
• src/hg/makeDb/trackDb/virus/wuhCor1/strainMuts.html
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    f12404d2efc298b76c7662b5269a96ebf19ceb32 Wed Jan 27 13:21:15 2021 -0800
    Exploratory composite of AA mutations, for cov2 strains of interest track. refs #26876
• src/hg/makeDb/trackDb/virus/wuhCor1/strains.ra
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    93ea38a5c1ef394d4a7d51cd44bc846a86904a70 Wed Jan 27 13:21:37 2021 -0800
    Exploratory composite of AA mutations, for cov2 strains of interest track. refs #26876
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    92a5025367260aca1acd09608d800d17f2f5c7ac Wed Jan 27 13:25:51 2021 -0800
    Fix cut/paste err. refs #26786
• src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra
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    f12404d2efc298b76c7662b5269a96ebf19ceb32 Wed Jan 27 13:21:15 2021 -0800
    Exploratory composite of AA mutations, for cov2 strains of interest track. refs #26876
• src/hg/utils/overlapSelect/chromAnn.c
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/chromAnn.h
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/overlapSelect.c
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/rowReader.c
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/rowReader.h
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBed3SelectTest.psl
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBed3Test.bed4+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBed6SelectTest.psl
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBed6Test.bed6+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBigPslSelectTest.bigPsl.bed
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraBigPslTest.bigPsl.bed
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraGenePredTest.gp+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/expected/extraPslTest.psl+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.bed4+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.bed6+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.bigPsl.bed
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.gp+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.psl
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/input/transMap.psl+meta
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/tests/makefile
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/hg/utils/overlapSelect/usage.txt
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    12d0bf30d4a9fbe7aee60fdf9e7f8827116ba400 Wed Jan 27 17:49:12 2021 -0800
    allow overlap select to ignore non-standard columns in BED as well as genePred and PSL, as often come with bigBed
• src/inc/portable.h
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    988cf706accde68911964e78b3e63a9c27ade512 Tue Jan 26 12:20:41 2021 -0800
    remove unused remoteFileExists()
• src/lib/osunix.c
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    988cf706accde68911964e78b3e63a9c27ade512 Tue Jan 26 12:20:41 2021 -0800
    remove unused remoteFileExists()
• src/product/mirrorManual.txt
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    bfc920a91a9dc0a179a4bdb0e89f198496460913 Fri Jan 29 15:22:41 2021 -0800
    Typo fix and replacing hgsid note with session note refs #26860
• src/utils/chromToUcsc/chromToUcsc
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    ad6ef3b792cf6a41a1a01191eee9d73aa68c9504 Tue Jan 26 06:49:35 2021 -0800
    update chromToUcsc to work with BAM files, refs #26839
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    83b6e55d2e100cb7c6e92e5c57d934040d8a524d Tue Jan 26 06:59:34 2021 -0800
    adding * as a valid chrom name to chromToUcsc, refs #26839
• src/utils/chromToUcsc/tests/expected/mm10.ebi.sam
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    ad6ef3b792cf6a41a1a01191eee9d73aa68c9504 Tue Jan 26 06:49:35 2021 -0800
    update chromToUcsc to work with BAM files, refs #26839
• src/utils/chromToUcsc/tests/in/mm10.ebi.sam.gz
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    dd7978582c73371183aa449a78df7c24113af46a Tue Jan 26 06:50:47 2021 -0800
    forgot a file in the previous commit
• src/utils/chromToUcsc/tests/makefile
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    ad6ef3b792cf6a41a1a01191eee9d73aa68c9504 Tue Jan 26 06:49:35 2021 -0800
    update chromToUcsc to work with BAM files, refs #26839
• src/utils/qa/weeklybld/buildEnv.csh
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    85a7810c3a3b38ab63d10e84434469d231bc225e Mon Feb 1 10:04:20 2021 -0800
    v410 preview2, refs #26867

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• files changed: 84