57d31ee9aede2bf610907285b05af8d9cbfe9bec markd Sun Mar 13 10:45:03 2022 -0700 added ability to override incorrect sizes often found in RepeatMaster alignments diff --git src/hg/utils/rmskAlignToPsl/tests/makefile src/hg/utils/rmskAlignToPsl/tests/makefile index e5a6c0a..a11c73f 100644 --- src/hg/utils/rmskAlignToPsl/tests/makefile +++ src/hg/utils/rmskAlignToPsl/tests/makefile @@ -1,34 +1,38 @@ kentSrc = ../../../.. include ../../../../inc/common.mk rmskAlignToPsl = ${DESTBINDIR}/rmskAlignToPsl # input/hg38.fa.align.tsv is from Dfam_2.0 all:: -test:: hg38Test mm39Test mm39ProbTest hg38BigRmskTest +test:: hg38Test mm39Test mm39ProbTest hg38BigRmskTest wrongSizeTest hg38Test: mkout ${rmskAlignToPsl} input/hg38.align.tsv output/$@.psl diff expected/$@.psl output/$@.psl mm39Test: mkout ${rmskAlignToPsl} input/mm39.align.tsv output/$@.psl diff expected/$@.psl output/$@.psl mm39ProbTest: mkout ${rmskAlignToPsl} input/mm39.prob.align.tsv output/$@.psl >output/$@.err 2>&1 diff expected/$@.psl output/$@.psl diff expected/$@.err output/$@.err hg38BigRmskTest: mkout ${rmskAlignToPsl} -bigRmsk input/hg38.dfam_3.3.bigRmskIn output/$@.psl diff expected/$@.psl output/$@.psl +wrongSizeTest: mkout + ${rmskAlignToPsl} -repSizes=input/wrongSize.sizes -bigRmsk input/wrongSize.bigRmskIn output/$@.psl + diff expected/$@.psl output/$@.psl + mkout: @mkdir -p output clean:: rm -rf output