be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/geneBounds/clusterGenes/tests/makefile src/hg/geneBounds/clusterGenes/tests/makefile
index cf48f4a..fb3eb9c 100644
--- src/hg/geneBounds/clusterGenes/tests/makefile
+++ src/hg/geneBounds/clusterGenes/tests/makefile
@@ -1,25 +1,25 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 clusterGenes = ${DESTBINDIR}/clusterGenes
 
 all:
 
 test: refSeqTest refSeqCdsTest trackNamesTest joinTest joinCdsTest \
 	overlapUseStrandTest overlapIgnoreStrandsTest \
-	ignoreBasesTest ignoreBasesCdsTest
+	ignoreBasesTest ignoreBasesCdsTest ignoreBasesTinyTest
 
 # 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
@@ -50,25 +50,31 @@
 
 # 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 -ignoreBases
 ignoreBasesTest: mkout
 	${clusterGenes} -ignoreBases=5 output/$@.gl no input/overlapCases.gp
 	diff -u expected/$@.gl output/$@.gl
 
 ignoreBasesCdsTest: mkout
 	${clusterGenes} -ignoreBases=5 -cds output/$@.gl no input/overlapCases.gp
 	diff -u expected/$@.gl output/$@.gl
 
+# -ignoreBases bases was discarding when overlap exceeded ignored, it should
+# still put in a cluster.
+ignoreBasesTinyTest: mkout
+	${clusterGenes} -ignoreBases=40 output/$@.gl no input/Mt-tRNA.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