All File Changes

v346_base to v347_preview (2017-03-13 to 2017-03-20) v347

• confs/hgwbeta.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7b0998aa2499c314faa74e6af37ed108a4bda38d Sun Mar 19 01:20:07 2017 -0700
    Installing updated hg.conf files from UCSC servers
• confs/rr.hg.conf
  • lines changed 1, context: html, text, full: html, text
    7b0998aa2499c314faa74e6af37ed108a4bda38d Sun Mar 19 01:20:07 2017 -0700
    Installing updated hg.conf files from UCSC servers
• src/hg/cirm/cdw/wrangle/maniMani/maniMani
  • lines changed 19, context: html, text, full: html, text
    834ec8124bbab40bd50b8f6d66c5e6bcff4a2012 Tue Mar 14 08:53:11 2017 -0700
    Adding in some changes asked for by Clay and Nick, maniMani
• src/hg/hgBlat/hgBlat.c
  • lines changed 2, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 4, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461
  • lines changed 1, context: html, text, full: html, text
    8eaa25172971c5628813fe2d761ca015c9a49416 Wed Mar 15 14:59:39 2017 -0700
    changed i.e. to e.g. on base position hgTrackUi. Refs #15027
  • lines changed 4, context: html, text, full: html, text
    1ec6923b8825dc073e01796be7e818e1e08c34ac Wed Mar 15 15:01:38 2017 -0700
    fix some problem with converage graphs
• src/hg/hgTracks/gencodeTracks.c
  • lines changed 8, context: html, text, full: html, text
    29792e6f4b5efdc09e3fc37b162ac1e6b356cf75 Mon Mar 13 11:47:34 2017 -0700
    add (filter activated) to labels for mRNA and EST tracks if filters are configured
• src/hg/hgTracks/hgTracks.c
  • lines changed 8, context: html, text, full: html, text
    29792e6f4b5efdc09e3fc37b162ac1e6b356cf75 Mon Mar 13 11:47:34 2017 -0700
    add (filter activated) to labels for mRNA and EST tracks if filters are configured
  • lines changed 1, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461
• src/hg/hgTracks/hgTracks.h
  • lines changed 3, context: html, text, full: html, text
    29792e6f4b5efdc09e3fc37b162ac1e6b356cf75 Mon Mar 13 11:47:34 2017 -0700
    add (filter activated) to labels for mRNA and EST tracks if filters are configured
• src/hg/hgTracks/pslTrack.c
  • lines changed 6, context: html, text, full: html, text
    29792e6f4b5efdc09e3fc37b162ac1e6b356cf75 Mon Mar 13 11:47:34 2017 -0700
    add (filter activated) to labels for mRNA and EST tracks if filters are configured
• src/hg/hgTracks/pubsTracks.c
  • lines changed 3, context: html, text, full: html, text
    29792e6f4b5efdc09e3fc37b162ac1e6b356cf75 Mon Mar 13 11:47:34 2017 -0700
    add (filter activated) to labels for mRNA and EST tracks if filters are configured
• src/hg/hgTracks/simpleTracks.c
  • lines changed 7, context: html, text, full: html, text
    1ec6923b8825dc073e01796be7e818e1e08c34ac Wed Mar 15 15:01:38 2017 -0700
    fix some problem with converage graphs
• src/hg/hgTracks/snakeTrack.c
  • lines changed 2, context: html, text, full: html, text
    52a82d9b8de09cc9e7f0d02de1bcd4090cb2c5f5 Mon Mar 13 15:14:50 2017 -0700
    fix bigPsl snakes on negative strand
  • lines changed 11, context: html, text, full: html, text
    3202c22c6702bbbaf211bd054403e2fbf3c8c071 Wed Mar 15 11:54:20 2017 -0700
    fix brain dead error I introduced in snake support. Also, clean up error handling.
• src/hg/hgVai/hgVai.c
  • lines changed 136, context: html, text, full: html, text
    41723d134f8b0c52c78705c2e5da97f8875e3cf6 Wed Feb 15 11:44:39 2017 -0800
    Added HGVS terms as variant input option in hgVai. refs #11460
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    61a6db3160c99a8fef6004db5c5c6402c07255a5 Tue Mar 14 16:31:59 2017 -0700
    fixed transmap preserving hgsqi when linking to another genome and fixed getting transmap custom display with V4 track names
  • lines changed 1, context: html, text, full: html, text
    519ce0fc9ae99aa8150751bcd69a77263a6d8ca0 Wed Mar 15 12:22:57 2017 -0700
    fix a possible problem with mirrors using a complicated path for their cgi's
  • lines changed 1, context: html, text, full: html, text
    a677e1b7b9860bc11dd767b80f3937f6ae3d32d3 Wed Mar 15 12:41:30 2017 -0700
    make sure that hgc is getting the right item to align in bigPsl support
  • lines changed 14, context: html, text, full: html, text
    e72544929e82244769e95ef2f969f87779f0cc5f Wed Mar 15 14:35:09 2017 -0700
    add version infor tag in the title for ncbiRefSeqOther track refs #13673
• src/hg/hgc/transMapClick.c
  • lines changed 10, context: html, text, full: html, text
    61a6db3160c99a8fef6004db5c5c6402c07255a5 Tue Mar 14 16:31:59 2017 -0700
    fixed transmap preserving hgsqi when linking to another genome and fixed getting transmap custom display with V4 track names
  • lines changed 2, context: html, text, full: html, text
    35a0506fd96116dd8edc2ab02522070fdcd8f54f Wed Mar 15 13:11:03 2017 -0700
    backed out previous change to link to transmap source assembly; it's not the correct fix
• src/hg/htdocs/FAQ/FAQdownloads.html
  • lines changed 24, context: html, text, full: html, text
    77b586dfa122a9014cd1d3c6d210ee8964c2c579 Fri Mar 17 15:38:28 2017 -0700
    Adding FAQ for obtaining GTF, refs #19087
• src/hg/htdocs/FAQ/FAQlink.html
  • lines changed 2, context: html, text, full: html, text
    1210ebff5d5ddb207be25db33e7533daf3a92d1c Tue Mar 14 09:14:24 2017 -0700
    Adding a link from the FAQ/FAQlink.html to the optional parameters section on the Custom Track Users Guide refs #19065
  • lines changed 6, context: html, text, full: html, text
    1b544494bb1883bfda0aabd3e36ea0c73a7a8b55 Tue Mar 14 09:55:05 2017 -0700
    Adding a link to wikipedia direct links UCSC page to FAQ/FAQlinks.html refs #19065
• src/hg/htdocs/goldenPath/help/bigBed.html
  • lines changed 192, context: html, text, full: html, text
    5d63dc9fc0de1877ff653167fa24f4cb4c547ff2 Tue Mar 14 23:28:40 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/bigChain.html
  • lines changed 151, context: html, text, full: html, text
    5d63dc9fc0de1877ff653167fa24f4cb4c547ff2 Tue Mar 14 23:28:40 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/bigGenePred.html
  • lines changed 179, context: html, text, full: html, text
    5d63dc9fc0de1877ff653167fa24f4cb4c547ff2 Tue Mar 14 23:28:40 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/bigMaf.html
  • lines changed 171, context: html, text, full: html, text
    5d63dc9fc0de1877ff653167fa24f4cb4c547ff2 Tue Mar 14 23:28:40 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/bigPsl.html
  • lines changed 144, context: html, text, full: html, text
    5d63dc9fc0de1877ff653167fa24f4cb4c547ff2 Tue Mar 14 23:28:40 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 196, context: html, text, full: html, text
    d04ba0b9632e96329068e907a2ae93c75f53c966 Wed Mar 15 01:03:50 2017 -0700
    More clean-up of the format, writing and consistency.
• src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html
  • lines changed 2, context: html, text, full: html, text
    5d24a3fe4fdcdc93c59f9a12e14839c1e6d0c5ee Mon Mar 13 10:21:11 2017 -0700
    Minor correction to example hub URL, refs #10015
  • lines changed 15, context: html, text, full: html, text
    7f542e5c6b2ebb914fcb53f1279c4f324d4473ad Thu Mar 16 09:06:49 2017 -0700
    Changes based on CR. Changed format of example headers, added link to trackDb doc, spelling corrections, refs #19050
• src/hg/htdocs/goldenPath/help/hubQuickStartAssembly.html
  • lines changed 1, context: html, text, full: html, text
    8edf586b034aecdbdd6546c52c93ff79817feb18 Tue Mar 14 08:59:18 2017 -0700
    Updating IP for genome-euro from .120 to .99 refs #19066
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 2, context: html, text, full: html, text
    6beb3759a5871735b17abee33372cfbdfeb59dde Wed Mar 15 15:44:01 2017 -0700
    Fixing the anchor for news archives and adding the news to the gateway page
  • lines changed 28, context: html, text, full: html, text
    f28d2025bc0d67e70a95f49465bd41cd5ae60fce Fri Mar 17 11:59:40 2017 -0700
    Adding announcement for release of new trackDb doc version, minor change to assembly annoucement from from same day, refs #1015
• src/hg/htdocs/indexNews.html
  • lines changed 6, context: html, text, full: html, text
    6beb3759a5871735b17abee33372cfbdfeb59dde Wed Mar 15 15:44:01 2017 -0700
    Fixing the anchor for news archives and adding the news to the gateway page
  • lines changed 13, context: html, text, full: html, text
    f28d2025bc0d67e70a95f49465bd41cd5ae60fce Fri Mar 17 11:59:40 2017 -0700
    Adding announcement for release of new trackDb doc version, minor change to assembly annoucement from from same day, refs #1015
• src/hg/htdocs/training/index.html
  • lines changed 45, context: html, text, full: html, text
    20b6a23e2fa18549753199c15f8ed43b5bf71d1b Wed Mar 15 14:33:42 2017 -0700
    dropping completed Regeneron workshop, adding detail abt HowardU, ESHG and WUStL
  • lines changed 16, context: html, text, full: html, text
    a9c0782773a40ec7ad49aa210f7c28224cf6b866 Wed Mar 15 15:58:50 2017 -0700
    Adding some user guides to the training page, and ability to call section with training#guides
• src/hg/htdocs/training/vids/index.html
  • lines changed 337, context: html, text, full: html, text
    f76b965b3e632d5508db040b32bd316e143b624f Fri Mar 17 14:26:20 2017 -0700
    rearranging video icons to put recent at the top. keeping copy of original in my sandbox as index.bak.html
• src/hg/inc/botDelay.h
  • lines changed 7, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461
• src/hg/inc/hgHgvs.h
  • lines changed 164, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
  • lines changed 2, context: html, text, full: html, text
    31dffd2604b7ba4ab85a2dc0d45246ef58838907 Wed Mar 15 13:59:23 2017 -0700
    Better warning message for HGVS protein terms pasted into hgVai. refs #11460 notes 30, 31.
• src/hg/js/hgVarAnnogrator.js
  • lines changed 4, context: html, text, full: html, text
    41723d134f8b0c52c78705c2e5da97f8875e3cf6 Wed Feb 15 11:44:39 2017 -0800
    Added HGVS terms as variant input option in hgVai. refs #11460
• src/hg/lib/bigBedFind.c
  • lines changed 1, context: html, text, full: html, text
    81e8b9cb578ac40b8cdd16e3ffa306b5b167d66f Sat Mar 18 12:30:15 2017 -0700
    allow bigBed trix searches to work on GBDB by checking for hgdownload as well as local files
• src/hg/lib/botDelay.c
  • lines changed 26, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461
• src/hg/lib/hgFind.c
  • lines changed 37, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/hgHgvs.c
  • lines changed 813, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
  • lines changed 10, context: html, text, full: html, text
    31dffd2604b7ba4ab85a2dc0d45246ef58838907 Wed Mar 15 13:59:23 2017 -0700
    Better warning message for HGVS protein terms pasted into hgVai. refs #11460 notes 30, 31.
• src/hg/lib/hgHgvsParse.c
  • lines changed 803, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt
  • lines changed 44, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/tests/expected/hgvs/validTerms.txt
  • lines changed 19, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/tests/hgvsTester.c
  • lines changed 3, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/lib/trashDir.c
  • lines changed 12, context: html, text, full: html, text
    706bb7eb367b92f9a1b3d56a7adb39e81eb13f77 Tue Mar 14 10:56:04 2017 -0700
    make trash dir for date decorated trash files
• src/hg/makeDb/doc/aquChr2/initialBuild.txt
  • lines changed 62, context: html, text, full: html, text
    332df58d52971b46fe073e4c9006ecd2aa029890 Mon Mar 13 15:02:42 2017 -0700
    adding ucscToRefSeq track table and chromAlias table refs #15096
• src/hg/makeDb/doc/bisBis1/initialBuild.txt
  • lines changed 84, context: html, text, full: html, text
    f585cc1c991318ee2db68e01035c8e807950c100 Tue Mar 14 15:25:29 2017 -0700
    adding ucscToRefSeq track and chromAlias table refs #15388
• src/hg/makeDb/doc/hg19.txt
  • lines changed 5, context: html, text, full: html, text
    b8ba0b857e4d1700a7fd22aefb93cfec1f2f0d21 Thu Mar 16 11:22:56 2017 -0700
    finish off rbest for micOch1 lastz swap refs #9871
• src/hg/makeDb/doc/mm10.txt
  • lines changed 244, context: html, text, full: html, text
    ba65cbde8c1d7b0d0192b2874425c2b96baf3be9 Sat Mar 18 17:06:51 2017 -0700
    lastz/chain/net for tupChi1 manPen1 aquChr2 bisBis1 refs #10146 #15515 #15096 #15388
• src/hg/makeDb/doc/nanPar1/initialBuild.txt
  • lines changed 62, context: html, text, full: html, text
    17ebb1433722faa6c415eea8701874aedf9030b0 Mon Mar 13 13:52:37 2017 -0700
    add ucscToRefSeq track and chromAlias table refs #15056
• src/hg/makeDb/doc/rn6.txt
  • lines changed 44, context: html, text, full: html, text
    606a0bb921980ae8e7b3b16cf290b802041abe55 Wed Mar 15 14:32:26 2017 -0700
    adding new cytoBandIdeo tracks refs #14583
• src/hg/makeDb/trackDb/human/chainNetLegacy.ra
  • lines changed 16, context: html, text, full: html, text
    823e98e5030b16ed02e991fa7e615b7558843002 Fri Mar 17 12:08:06 2017 -0700
    Attempting to update human trackDb so rn6 chain gets into placental composite and rn4 and rn5 get into legacy composite, refs #18656
  • lines changed 30, context: html, text, full: html, text
    8eade3c85cdd01a89451104afb367f30f0ccc70f Fri Mar 17 12:25:40 2017 -0700
    I had the stanzas in the chainNetLegacy file wrong, which is why rn5 was still showing up in the placental track, refs #18696
• src/hg/makeDb/trackDb/human/chainNetPlacental.ra
  • lines changed 2, context: html, text, full: html, text
    823e98e5030b16ed02e991fa7e615b7558843002 Fri Mar 17 12:08:06 2017 -0700
    Attempting to update human trackDb so rn6 chain gets into placental composite and rn4 and rn5 get into legacy composite, refs #18656
  • lines changed 1, context: html, text, full: html, text
    0d8c4490d924c6f05de1b4742bdb942449e44d74 Fri Mar 17 13:51:59 2017 -0700
    Woops don't need an alpha tag on chainNetRn6 on hg38 browser, refs #18656
• src/hg/makeDb/trackDb/human/chainNetRn6.ra
  • lines changed 15, context: html, text, full: html, text
    823e98e5030b16ed02e991fa7e615b7558843002 Fri Mar 17 12:08:06 2017 -0700
    Attempting to update human trackDb so rn6 chain gets into placental composite and rn4 and rn5 get into legacy composite, refs #18656
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.euarchontoglireChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    46bcc1e62b51d4038bc4692f5d6bc3d6c99da778 Mon Mar 13 10:47:01 2017 -0700
    changed panTro4 to panTro5
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.gliresChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    e5c4fd9844766a106dc472a9f9be4f582a289463 Fri Mar 17 13:16:45 2017 -0700
    Moving rn5 chain to mm10 legacy composite and rn6 chain to glires composite, refs #18656
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.previousVersionsChainNet.ra
  • lines changed 16, context: html, text, full: html, text
    e5c4fd9844766a106dc472a9f9be4f582a289463 Fri Mar 17 13:16:45 2017 -0700
    Moving rn5 chain to mm10 legacy composite and rn6 chain to glires composite, refs #18656
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    8575dea8534aecc0a9f350db82ace032f6f36a1b Wed Mar 15 14:50:00 2017 -0700
    not ready for NCBI refSeq composite yet refs #19072
• src/hg/makeDb/trackDb/mouse/mm10/trackDb.vertebrateChainNet.ra
  • lines changed 6, context: html, text, full: html, text
    c82c7c82a7ee9046097fb2c00314e40e670c10d0 Mon Mar 13 10:10:52 2017 -0700
    adding melGal5 to mm10 vertebrate track per refs #18739
• src/hg/makeDb/trackDb/rat/rn6/cons20way.html
  • lines changed 1, context: html, text, full: html, text
    c32d75066fe1d800ff88845a716c9dc3b24d2669 Thu Mar 16 11:32:16 2017 -0700
    Replacing link to prairie vole gateway page with link to 2bit file since micOch1 browser not yet released, refs #18656
• src/hg/makeDb/trackDb/rat/rn6/trackDb.20way.ra
  • lines changed 4, context: html, text, full: html, text
    f35f9381364db4b2c41706ad280cd1708df839e0 Wed Mar 15 10:50:54 2017 -0700
    Turning off chain/nets on rn6 by default, turning off cons elems and phastcons tracks by default, and deleting useless visibility line from chainNet.ra in preparation for 20way release, refs #18656
• src/hg/makeDb/trackDb/rat/rn6/trackDb.chainNet.ra
  • lines changed 1, context: html, text, full: html, text
    f35f9381364db4b2c41706ad280cd1708df839e0 Wed Mar 15 10:50:54 2017 -0700
    Turning off chain/nets on rn6 by default, turning off cons elems and phastcons tracks by default, and deleting useless visibility line from chainNet.ra in preparation for 20way release, refs #18656
• src/hg/makeDb/trackDb/rat/rn6/vertebrateChainNet.ra
  • lines changed 3, context: html, text, full: html, text
    f35f9381364db4b2c41706ad280cd1708df839e0 Wed Mar 15 10:50:54 2017 -0700
    Turning off chain/nets on rn6 by default, turning off cons elems and phastcons tracks by default, and deleting useless visibility line from chainNet.ra in preparation for 20way release, refs #18656
  • lines changed 6, context: html, text, full: html, text
    c153e49014a609d2691f4a1f62260ddf137f34dd Wed Mar 15 11:29:04 2017 -0700
    fixing default visibilities when chain/net track is turned on for rn6, refs #18656
• src/hg/oneShot/hgvsParse/hgvsParse.c
  • lines changed 174, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/oneShot/hgvsParse/makefile
  • lines changed 3, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/automation/makePushQSql.pl
  • lines changed 29, context: html, text, full: html, text
    804dd6394d7b3887ac18cccdf38899f9d31ccd7d Mon Mar 13 10:41:32 2017 -0700
    can now make redmine listings refs #10146
  • lines changed 21, context: html, text, full: html, text
    b0eb5441b698299a7d2e0b7292e6c86b90a8dc9c Thu Mar 16 15:32:19 2017 -0700
    add title line to the release log text refs #10146
• src/hg/utils/hgvsToVcf/hgvsToVcf.c
  • lines changed 84, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/makefile
  • lines changed 3, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/tests/expected/clinVarChanges.vcf
  • lines changed 49, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/tests/expected/testShifting.vcf
  • lines changed 34, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/tests/input/clinVarChanges.txt
  • lines changed 41, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/tests/input/testShifting.txt
  • lines changed 49, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/hgvsToVcf/tests/makefile
  • lines changed 24, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/hg/utils/phyloTrees/209way.nh
  • lines changed 35, context: html, text, full: html, text
    8d9be8b41f93ac2fe12894f97fd3a468503aaa8f Fri Mar 17 15:51:16 2017 -0700
    adjusting distances to equal the 191way refs #17545
• src/inc/dystring.h
  • lines changed 14, context: html, text, full: html, text
    b534e5e167df93880881df0478ecec0225fdf136 Wed Aug 31 17:01:24 2016 -0700
    This commit adds the capability to pick apart complex HGVS sequence change descriptions, and apply those changes to reference sequence, in order to translate HGVS nucleotide terms into a variant representation suitable for functional prediction in hgVai. VCF was chosen since it is easy to integrate into hgVai. refs #11460 Changes to existing code: * hgvsMapToGenome maps to BED6 instead of BED3 because we need to know strand in order to convert transcript changes into VCF forward-strand genomic changes. * hgvsMapToGenome maps insertions to zero-length points instead of 2-base ranges as in HGVS. New file hgHgvsParse.c contains a tokenizer and parser for HGVS sequence change descriptions; top-level interface is hgvsParseNucleotideChange. hgHgvs.c has new code to translate parsed HGVS nucleotide change(s) into VCF, optionally left-shifting ambiguous alignments (VCF convention, at odds with HGVS right-shifting convention); top-level interface is hgvsToVcfRow. New hgvsToVcf utility enables testing of corner cases and may come in handy as a command-line util. HGVS terms for testing have been taken from ClinVar and do not reflect the diversity of terms in the wild, nor do they cover the full HGVS spec. For example, the HGVS repeat notation can be parsed but not mapped to the genome because all of the ClinVar repeat terms that I looked at looked wonky to me and I believe the HGVS repeat notation is inherently error-prone. The repeat notation is supposed to use the position of the first repeat unit and to specify the number of repeated copies starting at that point (right-shifted if ambiguous). However, in ClinVar, sometimes the given repeat unit sequence did not match the reference sequence at the given position; sometimes the number of sepeats made sense only if they were not perfect repeats (some differing bases); sometimes ranges of repeat numbers were given. Also, the reference assembly's number of repeats can change from one assembly to the next. So it is hard given an HGVS repeat term to determine 1) whether it makes sense in relation to the reference assembly with/without fuzzy matching and 2) what the exact change is relative to the reference assembly. Insertions of inverted sequence from elsewhere in the same reference have not yet been tested. http://varnomen.hgvs.org/recommendations/DNA/variant/inversion/ gives some complicated examples like "g.122_123ins213_234invinsAins123_211inv" but I have not yet seen terms like that in the wild.
• src/inc/vcf.h
  • lines changed 10, context: html, text, full: html, text
    41723d134f8b0c52c78705c2e5da97f8875e3cf6 Wed Feb 15 11:44:39 2017 -0800
    Added HGVS terms as variant input option in hgVai. refs #11460
• src/lib/vcf.c
  • lines changed 90, context: html, text, full: html, text
    41723d134f8b0c52c78705c2e5da97f8875e3cf6 Wed Feb 15 11:44:39 2017 -0800
    Added HGVS terms as variant input option in hgVai. refs #11460
• src/utils/qa/bigPush.sh
  • lines changed 2, context: html, text, full: html, text
    14c9f085afb7d35391264411c7bac9ac2a21b94f Mon Mar 13 11:40:47 2017 -0700
    Minor change to usage message, no redmine
• src/utils/qa/checkTableStatus.csh
  • lines changed 3, context: html, text, full: html, text
    c98efac85a1dc478878b7af2c96a77ffa9423f31 Mon Mar 13 11:37:54 2017 -0700
    Correcting path for table status dumps, refs #19003
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    f740a7aaebd65aa5fd6192c35c84ba3d2053c527 Mon Mar 20 09:55:44 2017 -0700
    v347 preview1 refs #18964
• src/weblet/bottleneck/bottleneck.c
  • lines changed 28, context: html, text, full: html, text
    ce1164c7b5a0ae2e6acf9c25a411df4b4c36244e Wed Mar 15 14:24:23 2017 -0700
    Bottleneck server can now impose fractional penalties; hgTracks, hgTrackUi, and hgBlat take advantage, refs #19019, #18461

• lines changed: 5034
• files changed: 97