2c43bbe76a2350dfd358bbb5047237243dcb984e
markd
  Tue Nov 8 23:09:32 2022 -0800
added a test case and improved debug and clarified code.  However it was pointless, because there was not accutally a bug, just a confused user

diff --git src/hg/utils/overlapSelect/tests/makefile src/hg/utils/overlapSelect/tests/makefile
index 6dc4feb..7ada511 100644
--- src/hg/utils/overlapSelect/tests/makefile
+++ src/hg/utils/overlapSelect/tests/makefile
@@ -247,53 +247,59 @@
 colSelectStrand: mkout
 	${overlapSelect} -strand -selectCoordCols=1,2,3,4 -inCoordCols=3,4,5,6 \
 	    input/gene.select input/gene.clusters output/$@.cluster
 	${DIFF} expected/$@.cluster output/$@.cluster
 
 # stats output, by column, including name, ignoring strand
 colStats: mkout
 	${overlapSelect} -statsOutput -selectCoordCols=1,2,3,,0 -inCoordCols=3,4,5,,2 \
 	    input/gene.select input/gene.clusters output/$@.cluster
 	${DIFF} expected/$@.cluster output/$@.cluster
 
 ###
 # CDS overlap tests
 ###
 cdsOverlapTests: cdsOverlapCdsCds cdsOverlapCdsExon \
-		cdsOverlapExonCds noCdsSelect noCdsSelectNoOver
+		cdsOverlapExonCds noCdsSelect noCdsSelectNoOver \
+		cdsOverlapGpBed12
 
 # CDS doesn't overlap
 cdsOverlapCdsCds: mkout
 	${overlapSelect} -inCds -selectCds input/cdsOverlap1.gp input/cdsOverlap2.gp output/$@.gp
 	${DIFF} expected/$@.gp output/$@.gp
 
 cdsOverlapCdsExon: mkout
 	${overlapSelect} -inCds input/cdsOverlap1.gp input/cdsOverlap2.gp output/$@.gp
 	${DIFF} expected/$@.gp output/$@.gp
 
 cdsOverlapExonCds: mkout
 	${overlapSelect} -selectCds input/cdsOverlap1.gp input/cdsOverlap2.gp output/$@.gp
 	${DIFF} expected/$@.gp output/$@.gp
 
 # regression: select with CDS and a genePred with no CDS
 noCdsSelect: mkout
 	${overlapSelect} -selectCds input/noCds.gp input/noCds2.gp output/$@.gp
 	${DIFF} expected/$@.gp output/$@.gp
 noCdsSelectNoOver: mkout
 	${overlapSelect} -nonOverlapping -selectCds input/noCds.gp input/noCds2.gp output/$@.gp
 	${DIFF} expected/$@.gp output/$@.gp
 
+# regression dected overlapped in introns and UTR
+cdsOverlapGpBed12: mkout
+	${overlapSelect} -selectCds input/cds-overlap.gencode.gp input/cds-overlap.rmsk.bed output/$@.bed
+	${DIFF} expected/$@.bed output/$@.bed
+
 ###
 # -merge tests
 ###
 mergeTests: psl_over_NM_015110gpMerge psl_over_NM_001206bedMerge \
 	bed_over_NM_015110bedMerge colSelectMerge
 
 # select psls overlaping NM_015110 with gp and merge
 psl_over_NM_015110gpMerge: mkout
 	${overlapSelect} -mergeOutput -dropped=output/$@.drop.psl input/NM_015110.gp input/mrna.psl output/$@.psl
 	${DIFF} expected/$@.psl output/$@.psl
 	${DIFF} expected/$@.drop.psl output/$@.drop.psl
 
 # select psls overlaping NM_001206 with bed and merge
 psl_over_NM_001206bedMerge: mkout
 	${overlapSelect} -mergeOutput input/NM_001206.bed input/mrna.psl output/$@.psl