f0b2eab01fa6d080c92c0444ef84d482b75afec9
markd
  Mon Oct 5 17:31:06 2020 -0700
replaced the -minOverlappingBases option with -ignoreBases; -minOverlappingBases did not work correctly and would have requred major restructing of the code.  The -ignoreBases directly address the issue of minor overlap at the ends of transcripts

diff --git src/hg/geneBounds/clusterGenes/tests/makefile src/hg/geneBounds/clusterGenes/tests/makefile
index 4c399a9..cf48f4a 100644
--- src/hg/geneBounds/clusterGenes/tests/makefile
+++ src/hg/geneBounds/clusterGenes/tests/makefile
@@ -1,26 +1,25 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 clusterGenes = ${DESTBINDIR}/clusterGenes
 
 all:
 
 test: refSeqTest refSeqCdsTest trackNamesTest joinTest joinCdsTest \
-	overlapUseStrandTest overlapIgnoreStrandsTest
-
-# minOverlappingBasesTest minOverlappingCdsBasesTest
+	overlapUseStrandTest overlapIgnoreStrandsTest \
+	ignoreBasesTest ignoreBasesCdsTest
 
 # 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
@@ -42,35 +41,34 @@
 	${clusterGenes} -joinContained -cds -clusterBed=output/$@.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
-	${clusterGenes} -minOverlappingBases=30 output/$@.gl no input/minOverlapCases.gp
+# test of -ignoreBases
+ignoreBasesTest: mkout
+	${clusterGenes} -ignoreBases=5 output/$@.gl no input/overlapCases.gp
 	diff -u expected/$@.gl output/$@.gl
 
-minOverlappingCdsBasesTest: mkout
-	${clusterGenes} -minOverlappingBases=30 -cds output/$@.gl no input/minOverlapCases.gp
+ignoreBasesCdsTest: mkout
+	${clusterGenes} -ignoreBases=5 -cds output/$@.gl no input/overlapCases.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