dddc3258aec53ba33f27a2233816cc02a42b940d
markd
  Wed Sep 30 12:41:38 2020 -0700
refactor to simplified code in prep for fixing minOverlapping functionality

diff --git src/hg/geneBounds/clusterGenes/tests/makefile src/hg/geneBounds/clusterGenes/tests/makefile
index 1ed7b1a..4c399a9 100644
--- src/hg/geneBounds/clusterGenes/tests/makefile
+++ src/hg/geneBounds/clusterGenes/tests/makefile
@@ -1,70 +1,76 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 clusterGenes = ${DESTBINDIR}/clusterGenes
 
 all:
 
 test: refSeqTest refSeqCdsTest trackNamesTest joinTest joinCdsTest \
-	overlapUseStrandTest overlapIgnoreStrandsTest \
-	minOverlappingBasesTest
+	overlapUseStrandTest overlapIgnoreStrandsTest
+
+# minOverlappingBasesTest minOverlappingCdsBasesTest
 
 # test files blatRefSeq.gp  ncbiRefSeq.gp
 #  chr1:11,689,948-12,078,317 - some basic genes
 #    blat NM_138346.1 edited to have shorter CDS, different exon boundries
 #    both NM_000302.2 edited so CDS doesn't overlap
 #  chr4:71,201,777-71,250,403 - a merged cluster
 
 refSeqTest: mkout
 	${clusterGenes} -conflicted -clusterBed=output/$@.bed -flatBed=output/$@.flat.bed output/$@.gl no input/blatRefSeq.gp input/ncbiRefSeq.gp
 	diff -u expected/$@.gl output/$@.gl
 	diff -u expected/$@.bed output/$@.bed
 	diff -u expected/$@.flat.bed output/$@.flat.bed
 
 refSeqCdsTest: mkout
 	${clusterGenes} -cds -clusterBed=output/$@.bed -clusterTxBed=output/$@.tx.bed output/$@.gl no input/blatRefSeq.gp input/ncbiRefSeq.gp
 	diff -u expected/$@.gl output/$@.gl
 	diff -u expected/$@.bed output/$@.bed
 	diff -u expected/$@.tx.bed output/$@.tx.bed
 
 trackNamesTest: mkout
 	${clusterGenes} -conflicted -cds -trackNames output/$@.gl no fred input/blatRefSeq.gp barney input/ncbiRefSeq.gp
 	diff -u expected/$@.gl output/$@.gl
 
 joinTest: mkout
 	${clusterGenes} -joinContained -clusterBed=output/$@.bed -flatBed=output/$@.flat.bed output/$@.gl no input/blatRefSeq.gp input/ncbiRefSeq.gp input/joinSmall.gp
 	diff -u expected/$@.gl output/$@.gl
 	diff -u expected/$@.bed output/$@.bed
 	diff -u expected/$@.flat.bed output/$@.flat.bed
 
 joinCdsTest: mkout
 	${clusterGenes} -joinContained -cds -clusterBed=output/$@.bed -flatBed=output/$@.flat.bed output/joinCdsTest.gl no input/blatRefSeq.gp input/ncbiRefSeq.gp input/joinSmall.gp
 	diff -u expected/$@.gl output/$@.gl
 	diff -u expected/$@.bed output/$@.bed
 	diff -u expected/$@.flat.bed output/$@.flat.bed
 
 # overlaping genes blocks on opposite stands
 overlapUseStrandTest: mkout
 	${clusterGenes} -trackNames output/$@.gl no genes input/overlapDiffStrands.gp
 	diff -u expected/$@.gl output/$@.gl
 
 # overlaping genes blocks on opposite stands, but ignore strand
 overlapIgnoreStrandsTest: mkout
 	${clusterGenes} -ignoreStrand -trackNames output/$@.gl no genes input/overlapDiffStrands.gp
 	diff -u expected/$@.gl output/$@.gl
 
 # test of -minOverlappingBases
+# test case was one were original implmentation put a transcript in two clusters
 minOverlappingBasesTest: mkout
-	${clusterGenes} -minOverlappingBases=10 output/$@.gl no input/smallOverlap.gp
+	${clusterGenes} -minOverlappingBases=30 output/$@.gl no input/minOverlapCases.gp
+	diff -u expected/$@.gl output/$@.gl
+
+minOverlappingCdsBasesTest: mkout
+	${clusterGenes} -minOverlappingBases=30 -cds output/$@.gl no input/minOverlapCases.gp
 	diff -u expected/$@.gl output/$@.gl
 
 mkout:
 	${MKDIR} output
 
 clean:
 	rm -rf output
 
 # run valgrind
 valgrindOpts =  -v --skin=memcheck --num-callers=20 --leak-check=yes --leak-resolution=med --show-reachable=yes
 valgrind:  mkout
 	valgrind ${valgrindOpts} ${clusterGenes} -clusterBed=output/refSeqTest.bed -flatBed=output/refSeqTest.flat.bed output/refSeqTest.gl no input/blatRefSeq.gp input/ncbiRefSeq.gp