51aef9631658a9ec173d7c5aa8989738ae4a71ba braney Thu Oct 7 17:01:53 2021 -0700 add a fix to a bug where liftOver elements with zero size that did *not* fit into a chain were flagges as an error rather than just marked as missing diff --git src/hg/liftOver/tests/makefile src/hg/liftOver/tests/makefile index e862075..00a5ca4 100644 --- src/hg/liftOver/tests/makefile +++ src/hg/liftOver/tests/makefile @@ -1,171 +1,179 @@ kentSrc = ../../.. include ../../../inc/common.mk # make VERBOSE=-verbose=2 will echo out positions as they convert -test: bin bedPlus3 bed8 bed12 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug +test: bin bedPlus3 bed8 bed12 simpleTest minus enm001 chuckTest chuckBigTest enr223 scaffoldEndBug zeroWidth # tests too slow to use in default test suite testSlow: mm3 multiple liftOver=${DESTBINDIR}/liftOver liftOverMerge=${DESTBINDIR}/liftOverMerge +zeroWidth: mkdirs + ${liftOver} \ + input/zeroWidth.bed \ + /cluster/data/hg19/bed/liftOver/hg19ToHg38.over.chain.gz \ + output/zeroWidth.good.bed output/zeroWidth.bad.bed 2> /dev/null + cat output/zeroWidth.{good,bad}.bed | \ + diff - expected/zeroWidth.bed 1>&2 + bed12: mkdirs ${liftOver} \ input/bed12.bed \ /cluster/data/hg38/bed/liftOver/hg38ToPanTro6.over.chain.gz \ output/bed12.good.bed output/bed12.bad.bed 2> /dev/null cat output/bed12.{good,bad}.bed | \ diff - expected/bed12.bed 1>&2 bed8: mkdirs ${liftOver} \ input/bed8.bed \ /cluster/data/hg16/bed/liftOver/hg16ToHg17.over.chain.gz \ output/bed8.good.bed output/bed8.bad.bed 2> /dev/null cat output/bed8.{good,bad}.bed | \ diff - expected/bed8.bed 1>&2 bin: mkdirs ${liftOver} -hasBin -bedPlus=6\ input/bin.bed \ /cluster/data/mm2/bed/liftOver/mm2ToMm5.over.chain.gz \ output/bin.good.bed output/bin.bad.bed 2> /dev/null cat output/bin.{good,bad}.bed | \ diff - expected/bin.bed 1>&2 bedPlus3: mkdirs ${liftOver} -bedPlus=3 \ input/bedPlus.bed \ /cluster/data/mm2/bed/liftOver/mm2ToMm5.over.chain.gz \ output/bedPlus3.good.bed output/bedPlus3.bad.bed 2> /dev/null cat output/bedPlus3.{good,bad}.bed | \ diff - expected/bedPlus3.bed 1>&2 simpleTest: mkdirs ${liftOver} \ input/mouseRegions.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chr16.chain \ output/mouseRegions.good.bed \ output/mouseRegions.bad.bed 2> /dev/null cat output/mouseRegions.{good,bad}.bed | \ diff - expected/mouseRegions.bed 1>&2 minus: mkdirs ${liftOver} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple ${VERBOSE} \ input/enr223.S.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chr6.chain \ output/enr223.S.good.bed \ output/enr223.S.bad.bed 2> /dev/null cat output/enr223.S.{good,bad}.bed | \ diff - expected/enr223.S.bed 1>&2 # test w/o multiple enm001: mkdirs ${liftOver} -minMatch=.01 \ input/enm001.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chr7.chain \ output/enm001.good.bed output/enm001.bad.bed 2> /dev/null cat output/enm001.{good,bad}.bed | \ diff - expected/enm001.bed 1>&2 chuckTest: mkdirs ${liftOver} \ input/chuckTest.bed \ /cluster/data/mm2/bed/liftOver/mm2.mm5.liftOver/over/chr19.chain \ output/chuckTest.good.bed output/chuckTest.bad.bed 2> /dev/null cat output/chuckTest.{good,bad}.bed | \ diff - expected/chuckTest.bed 1>&2 chuckBigTest: mkdirs ${liftOver} \ input/chuckBigTest.bed \ /cluster/data/mm2/bed/liftOver/mm2ToMm5.over.chain.gz \ output/chuckBigTest.good.bed output/chuckBigTest.bad.bed 2> /dev/null cat output/chuckBigTest.{good,bad}.bed | \ diff - expected/chuckBigTest.bed 1>&2 # missing expected file m7rat: mkdirs ${liftOver} ${VERBOSE} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple \ input/m7rat.bed \ /cluster/data/hg16/bed/blastz.rn3/axtChain/subset/chr19.chain \ output/m7rat.good.bed output/m7rat.bad.bed 2> /dev/null ${liftOverMerge} ${VERBOSE} -mergeGap=2000 \ output/m7rat.good.bed output/m7rat.merged.bed cat output/m7rat.merged.bed | \ diff - expected/m7rat.bed 1>&2 # problem with config setting needed to access chain table m4mouse: mkdirs ${liftOver} ${VERBOSE} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple -chainTable=hg16.chainMm5\ input/m4mouse.bed \ /cluster/data/hg16/bed/blastz.mm5/axtChain/subset/chr22.chain \ output/m4mouse.good.bed output/m4mouse.bad.bed 2> /dev/null cat output/m4mouse.{good,bad}.bed | \ diff - expected/m4mouse.bed 1>&2 # differs from expected -- it doesn't merge (this function done by # liftOverMerge now ? mergeTest: enm006 enm006: mkdirs ${liftOver} ${VERBOSE} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple \ input/enm006.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chrX.chain \ output/enm006.good.bed output/enm006.bad.bed 2> /dev/null cat output/enm006.{good,bad}.bed | \ diff - expected/enm006.bed 1>&2 # missing expected file enr112: mkdirs ${liftOver} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple ${VERBOSE} \ input/enr112.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chr2.chain \ output/enr112.good.bed \ output/enr112.bad.bed 2> /dev/null cat output/enr112.{good,bad}.bed | \ diff - expected/enr112.bed 1>&2 # bug where genePred going at the exact end of a scaffold was not mapped scaffoldEndBug: ${liftOver} -genePred ${VERBOSE} input/scaffoldEndBug.gp input/scaffoldEndBug.chain \ output/$@.good.gp output/$@.bad.gp 2> /dev/null cat output/$@.{good,bad}.gp | diff - expected/$@.gp 1>&2 orderTest: enr223 enr223: mkdirs ${liftOver} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple ${VERBOSE} \ input/enr223.bed \ /cluster/data/hg16/bed/blastz.mm3/axtChain/subset/chr6.chain \ output/enr223.good.bed \ output/enr223.bad.bed 2> /dev/null cat output/enr223.{good,bad}.bed | \ diff - expected/enr223.bed 1>&2 # too slow -- don't use in default test suite mm3: mkdirs ${liftOver} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple ${VERBOSE}\ /cluster/data/hg16/bed/encodeRegions/encodeRegions.bed \ /cluster/data/hg16/bed/liftOver/hg16Tomm3.chain \ output/mm3.all.good.bed \ output/mm3.all.bad.bed cat output/mm3.all.{good,bad}.bed | \ diff - expected/mm3.all.bed 1>&2 # too slow -- don't use in default test suite multiple: mkdirs ${liftOver} -minMatch=.01 minSizeT=4000 minSizeQ=20000 -multiple ${VERBOSE}\ input/mm3.multiple.bed \ /cluster/data/hg16/bed/liftOver/hg16Tomm3.chain \ output/mm3.multiple.good.bed \ output/mm3.multiple.bad.bed cat output/mm3.multiple.{good,bad}.bed | \ diff - expected/mm3.multiple.bed 1>&2 mkdirs: mkdir -p output clean: rm -fr output