6ec964d05444b3c2f8147cd678de79ec5254b97a hiram Wed Feb 27 15:49:57 2019 -0800 output data from bigBed and bigWig track types for native database track refs #18869 diff --git src/hg/hubApi/hubApi.c src/hg/hubApi/hubApi.c index 55fb6c2..6f40732 100644 --- src/hg/hubApi/hubApi.c +++ src/hg/hubApi/hubApi.c @@ -578,48 +578,57 @@ slSort(&helList, hashElCmpIntValDesc); for (hel = helList; hel; hel = hel->next) { hPrintf("
  • %d - %s
    • \n", ptToInt(hel->val), hel->name); } hPrintf(" \n"); } hPrintf("\n"); hPrintf("

    \n"); } // static void tracksForUcscDb(char * db) static void showExamples(char *url, struct trackHubGenome *hubGenome, char *ucscDb) { hPrintf("

    Example URLs to return json data structures:

    \n"); + +hPrintf("

    listing functions

    \n"); hPrintf("
      \n"); hPrintf("
    1. list public hubs /cgi-bin/hubApi/list/publicHubs
      2. \n"); hPrintf("
    2. list database genomes /cgi-bin/hubApi/list/ucscGenomes
      3. \n"); hPrintf("
    3. list genomes from specified hub /cgi-bin/hubApi/list/hubGenomes?hubUrl=%s
      4. \n", url, url); hPrintf("
    4. list tracks from specified hub and genome /cgi-bin/hubApi/list/tracks?hubUrl=%s&genome=%s
      5. \n", url, url, hubGenome->name, url, hubGenome->name); hPrintf("
    5. list tracks from specified UCSC database /cgi-bin/hubApi/list/tracks?db=%s
      6. \n", ucscDb, ucscDb); hPrintf("
    6. list chromosomes from specified UCSC database /cgi-bin/hubApi/list/chromosomes?db=%s
      7. \n", ucscDb, ucscDb); hPrintf("
    7. list chromosomes from specified track from UCSC databaset /cgi-bin/hubApi/list/chromosomes?db=%s&track=gap
      8. \n", ucscDb, ucscDb); +hPrintf("
    \n"); + +hPrintf("

    getData functions

    \n"); +hPrintf("
      \n"); hPrintf("
    1. get sequence from specified database and chromosome /cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM
      2. \n", ucscDb, ucscDb); hPrintf("
    2. get sequence from specified database, chromosome with start,end coordinates /cgi-bin/hubApi/getData/sequence?db=%s&chrom=chrM&start=0&end=128
      3. \n", ucscDb, ucscDb); hPrintf("
    3. get entire track data from specified database and track name (gold == Assembly) /cgi-bin/hubApi/getData/track?db=%s&track=gold
      4. \n", ucscDb, ucscDb); hPrintf("
    4. get track data from specified database, chromosome and track name (gold == Assembly) /cgi-bin/hubApi/getData/track?db=%s&chrom=chrM&track=gold
      5. \n", ucscDb, ucscDb); -hPrintf("
    5. get track data from specified database, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?db=%s&chrom=chr1&track=gold&start=107680&end=186148
      6. \n", ucscDb, ucscDb); +hPrintf("
    6. get track data from specified database, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gold&start=107680&end=186148
      7. \n", defaultDb, defaultDb); hPrintf("
    7. get entire track data from specified hub and track name /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt&genome=hg19&track=ultraConserved
      8. \n"); hPrintf("
    8. get track data from specified hub, chromosome and track name (full chromosome) /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrCp&track=assembly_
      9. \n"); hPrintf("
    9. get track data from specified hub, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chr1&track=assembly_&start=0&end=14309681
      10. \n"); hPrintf("
    10. get all track data from specified hub and track name /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&track=gc5Base
      11. \n"); hPrintf("
    11. get track data from specified hub, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrMt&track=gc5Base&start=143600&end=143685
      12. \n"); +hPrintf("
    12. get bigWig track data from specified database, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?db=%s&chrom=chrI&track=gc5BaseBw&start=107680&end=186148
      13. \n", defaultDb, defaultDb); +hPrintf("
    13. get bigBed track data from specified database, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?db=%s&chrom=chrII&track=ncbiRefSeqOther&start=14334626&end=14979625
      14. \n", defaultDb, defaultDb); + hPrintf("
    \n"); hPrintf("

    Example URLs to generate errors:

    \n"); hPrintf("
  • get track data from specified hub, chromosome, track name, start and end coordinates /cgi-bin/hubApi/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt&genome=_araTha1&chrom=chrI&track=assembly_&start=0&end=14309681
    • \n"); hPrintf("
      \n"); hPrintf("
    \n"); } /* static void showExamples() */ static void showCartDump() /* for information purposes only during development, will become obsolete */ { hPrintf("

    cart dump

    "); hPrintf("
    \n");
 cartDump(cart);
 hPrintf("
    \n");