e813f6c7cfd2f8f110266c0824062964322d62a3
markd
  Wed Sep 20 00:01:21 2023 -0700
fixed problems handling overlapping PSL blocks caused by protein to NA alignemtns. Now handles internal coversions create overlapoing blocks

diff --git src/utils/pslMap/tests/makefile src/utils/pslMap/tests/makefile
index 19a1d92..e57e0db 100644
--- src/utils/pslMap/tests/makefile
+++ src/utils/pslMap/tests/makefile
@@ -2,31 +2,31 @@
 include ${kentSrc}/inc/common.mk
 
 #pslMap = valgrind --tool=memcheck --num-callers=25 pslMap
 pslMap = ${DESTBINDIR}/pslMap
 pslSwap = ${DESTBINDIR}/pslSwap
 blastToPsl = ${DESTBINDIR}/blastToPsl
 pslCheck = ${DESTBINDIR}/pslCheck
 chainSwap = ${DESTBINDIR}/chainSwap
 
 all:
 
 test:	gapBoth mrnaMrnaMap mrnaMrnaXMap mrnaMapOver mrnaMapOverSwap \
 	mrnaMapOverChain mrnaMapOverChainSwap testMapFileWithInQName \
 	kgProt negQChain testProtPort_ProtNa testProtPort_ProtProt \
 	testProtNa_NaNa testProtProt_NaNa \
-	testTypeErr
+	testTypeErr testProtTrans
 
 # basic tests of protein -> mrna -> genome mapping
 kgProt: mkdirs
 	${blastToPsl} input/kgProtMRna.blast output/kgProtMRna.psl
 	${pslMap} output/kgProtMRna.psl input/kgMRna.psl output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # this generated a gap in both query and target
 gapBoth: mkdirs
 	${blastToPsl} input/gapBothProtMRna.blast output/gapBothProtMRna.psl
 	${pslMap} output/gapBothProtMRna.psl input/gapBothMRna.psl output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
@@ -122,20 +122,27 @@
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # prot_prot   na_na       cds_na
 testProtProt_NaNa: mkdirs
 	${pslMap} -inType=prot_prot -mapType=na_na input/spAnnotIso.psl expected/testProtNa_NaNa.psl output/$@.psl
 	${pslCheck} -verbose=0 output/$@.psl
 	diff -u expected/$@.psl output/$@.psl
 
 # implied types will not work with prot_na map:
 #    prot_prot   prot_na     cds_na
 testTypeErr: mkdirs
 	if ${pslMap} input/spAnnotIso.psl input/spGencode.psl output/$@.psl  2> output/$@.err ; then  echo "Error: should have failed" >&2; false ; else true ; fi
 	diff expected/$@.err output/$@.err
 
+# bug where swissprot feature to protein is mapped via protein to transcript, genereated
+# an invalid PSL with an overlapping block
+testProtTrans: mkdirs
+	${pslMap} -inType=prot_prot -mapType=prot_na input/annotProt.psl input/protGencode.psl output/$@.psl
+	${pslCheck} -verbose=0 output/$@.psl
+	diff -u expected/$@.psl output/$@.psl
+
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output