527d5b5e1e77777e67a1f69d19e615e850258570 hiram Tue Apr 30 09:46:00 2019 -0700 fixup wiggle output itemCount refs #18869 diff --git src/hg/hubApi/tests/makefile src/hg/hubApi/tests/makefile index 345c7ff..ab9a9f7 100644 --- src/hg/hubApi/tests/makefile +++ src/hg/hubApi/tests/makefile @@ -1,33 +1,35 @@ test:: test0 test1 test2 test3 test4 test5 test6 test7 test8 test9 test10 \ - test11 test12 test13 test14 test15 test16 test17 test18 test19 \ - test21 test22 test23 test26 \ - test27 test28 test29 test30 \ - test31 test39 test40 \ - test41 test42 test42 getSequence errorTests + test11 test12 test13 test14 test15 test16 test19 test21 test22 test23 \ + test26 test27 test28 test29 test30 test31 test39 test40 \ + listFunctions getFunctions getSequence wigData errorTests -all:: listFunctions getFunctions getSequence errorTests +all:: listFunctions getFunctions getSequence wigData errorTests listFunctions: test1 test2 test3 test4 test5 test22 test23 test30 test31 getFunctions: test6 test7 test8 test9 test10 test11 test12 test13 test14 \ - test15 test16 test17 test18 test19 test21 test26 test27 test28 \ + test15 test16 test19 test21 test26 test27 test28 \ test29 test39 test40 test41 test42 getSequence: getSeq01 getSeq02 getSeq03 +wigData: wig01 wig02 wig03 wig04 wig05 wig06 wig07 wig08 wig09 wig10 \ + wig11 wig12 wig13 wig14 wig15 wig16 wig17 wig18 wig19 wig20 \ + wig21 wig22 wig23 wig24 + errorTests: err01 err02 err03 err04 err05 err06 err07 err08 err09 err10 \ err11 err12 err13 err14 err15 err16 err17 err18 err19 err20 \ err21 err22 err23 err24 err25 err26 err27 err28 err29 setOutput: @if [ ! -d testOutput ]; then mkdir testOutput; fi clean:: rm -f testOutput/*.gz rmdir testOutput # exclude these lines from the JSON output for comparison with expected excludeLines = downloadTime|dataTime # testing /list/noSubCommand, /list/publicHubs and /list/ucscGenomes @@ -104,42 +106,30 @@ # testing /getData/track? hubUrl Bejerano &track=ultraConserved track hub test14: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1 track hub test15: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl Bejerano &track=ultraConserved&chrom=chr1&start=N&end=M track hub test16: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -track="ultraConserved" -chrom="chr1" -start=10600000 -end=10800000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# wiggle data from a track hub -# testing /getData/track? hubUrl Plants &track=gc5Base_&chrom=chrCp&start=1&end=1024 assembly hub -test17: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# bigWig data from a database -# /getData/track? genome=galGal6 &track=gc5BaseBw&chrom=chr1&start=1&end=1024 -test18: setOutput - @./jsonConsumer.pl -endpoint="/getData/track" -genome="galGal6" -track="gc5BaseBw" -chrom="chr1" -start=1 -end=1024 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - # bigBed data from a database # /getData/track? genome=galGal6 &track=ncbiRefSeqOther&chrom=chr1&start=750000&end=5700000 test19: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -genome="galGal6" -track="ncbiRefSeqOther" -chrom="chr1" -start=750000 -end=55700000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # wiggle data from a database where the SQL table name is different than the # track name # /getData/track? genome=hg19 &track=wgEncodeRegMarkH3k4me1H1hesc&chrom=chr1&start=62300000&end=62301000 test21: setOutput @./jsonConsumer.pl -endpoint="/getData/track" -genome="hg19" -track="wgEncodeRegMarkH3k4me1H1hesc" -chrom="chr1" -start=62300000 -end=62301000 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes? hubUrl genome=_araTha1 test22: setOutput @@ -184,42 +174,30 @@ test31: setOutput @./jsonConsumer.pl -endpoint="/list/tracks" -genome="ce11" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation test39: setOutput @./jsonConsumer.pl -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track?genome=ce4&track=gold for split table operation # plus jsonArrayOutput test40: setOutput @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce4" -track="gold" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz -# testing /getData/track?genome=ce11&track=gc5BaseBw - bigWig data output -# plus jsonArrayOutput -test41: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce11" -track="gc5BaseBw" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - -# testing /getData/track?genome=ce6&track=gc5Base - wiggle database table -# plus jsonArrayOutput -test42: setOutput - @./jsonConsumer.pl -jsonOutputArrays -maxItemsOutput=123 -endpoint="/getData/track" -genome="ce6" -track="gc5Base" | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz - @zdiff expected/$@.gz testOutput/$@.gz - ############################################################################### # /getData/sequence testing ############################################################################### # testing /getData/sequence? hubUrl genome=hg19&chrom=chrCp&start=4321&end=5647 getSeq01: setOutput @printf "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -chrom="chrCp" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/sequence? hubUrl Bejerano genome=hg19&chrom=chrM&start=4321&end=5647 getSeq02: setOutput @printf "### $@ " @./jsonConsumer.pl -endpoint="/getData/sequence" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt" -genome="hg19" -chrom="chrM" -start=4321 -end=5678 | egrep -v "${excludeLines}" | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz @@ -398,15 +376,159 @@ @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=assembly_;genome=araTha1_;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1_ -track=assembly_ 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /getData/track? hubUrl incorrect track specified err28: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/getData/track?track=_assembly;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'\n" @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=_araTha1 -track=_assembly 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz # testing /list/chromosomes hubUrl bad genome name err29: setOutput @printf "### $@ 'https://hgwdev-api.gi.ucsc.edu/list/chromosomes?genome=araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt'" @./jsonConsumer.pl -endpoint="/list/chromosomes" -hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt -genome=araTha1 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/list#/list#;' | gzip -c > testOutput/$@.gz @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file +wig01: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom specified +wig02: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIV -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom start,end specified +wig03: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIII;start=12345;end=45678;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIII -start=12345 -end=45678 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic bigWig with table and bigWig file +wig04: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom specified +wig05: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIV;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIV -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom start,end specified +wig06: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIII;start=12345;end=45678;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIII -start=12345 -end=45678 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track without a database table, just a bigDataUrl +wig07: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track without a database table, just a bigDataUrl with chrom +wig08: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chr19;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chr19 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track with no database table, just a bigDataUrl with chrom,start,end +wig09: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chrX;start=123456;end=456789;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chrX -start=123456 -end=456789 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file +wig10: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file, with chrom +wig11: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;chrom=chrCp;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file, with chrom, start, end +wig12: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;chrom=chrCp;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=5647;start=1234;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -start=1234 -end=5647 -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file, with jsonArrayOutput +wig13: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;maxItemsOutput=5;jsonOutputArrays=1'\n" + @./jsonConsumer.pl -jsonOutputArrays -endpoint="/getData/track" -genome=ce4 -track=gc5Base -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom specified +wig14: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIV;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIV -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom start,end specified +wig15: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5Base;genome=ce4;chrom=chrIII;start=12345;end=45678;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce4 -track=gc5Base -chrom=chrIII -start=12345 -end=45678 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic bigWig with table and bigWig file +wig16: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom specified +wig17: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIV;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIV -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# classic wiggle with wig table and wib file with chrom start,end specified +wig18: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gc5BaseBw;genome=ce11;chrom=chrIII;start=12345;end=45678;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=ce11 -track=gc5BaseBw -chrom=chrIII -start=12345 -end=45678 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track without a database table, just a bigDataUrl +wig19: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track without a database table, just a bigDataUrl with chrom +wig20: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chr19;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chr19 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# a bigWig track with no database table, just a bigDataUrl with chrom,start,end +wig21: setOutput + @printf "### $@ 'https://api-test.gi.ucsc.edu/getData/track?track=gnomadGenomesMeanCoverage;genome=hg19;chrom=chrX;start=123456;end=456789;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -genome=hg19 -track=gnomadGenomesMeanCoverage -chrom=chrX -start=123456 -end=456789 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file +wig22: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file, with chrom +wig23: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;chrom=chrCp;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz + +# wiggle data from a track hub bigWig file, with chrom, start, end +wig24: setOutput + @printf "### $@ 'https://hgwdev-hiram.gi.ucsc.edu/cgi-bin/hubApi/getData/track?track=gc5Base_;chrom=chrCp;genome=_araTha1;hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;end=5647;start=1234;jsonOutputArrays=1;maxItemsOutput=5'\n" + @./jsonConsumer.pl -endpoint="/getData/track" -hubUrl="http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt" -genome="_araTha1" -track="gc5Base_" -chrom="chrCp" -start=1234 -end=5647 -jsonOutputArrays -maxItemsOutput=5 2>&1 | egrep -v "${excludeLines}" | sed -e 's#https://.*/getData#/getData#;' | gzip -c > testOutput/$@.gz + @zdiff expected/$@.gz testOutput/$@.gz