e6cd18ccbe6e255de8cb54bc70da0e42fe9a73b5
markd
  Mon Aug 17 19:17:10 2020 -0700
add report of location of frameshifts for use by CAT

diff --git src/hg/utils/transMapPslToGenePred/tests/makefile src/hg/utils/transMapPslToGenePred/tests/makefile
index 2953a13..e9ff777 100644
--- src/hg/utils/transMapPslToGenePred/tests/makefile
+++ src/hg/utils/transMapPslToGenePred/tests/makefile
@@ -1,50 +1,65 @@
 kentSrc = ../../../..
 include ../../../../inc/common.mk
 
 transMapPslToGenePred = ${DESTBINDIR}/transMapPslToGenePred
 
 diff = diff -u
 
 all:
 
 test: musTest nonCodingFillTest codingFillTest fillTest fill30Test \
-	cds2InsertTest
-	${MAKE} clean
+	cds2InsertTest tmAstMex1Tests
 
 musTest: mkdirs
-	${transMapPslToGenePred} input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -frameShifts=output/$@.fs.tsv input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
 
 nonCodingFillTest: mkdirs
-	${transMapPslToGenePred} -nonCodingGapFillMax=10 input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -nonCodingGapFillMax=10 -frameShifts=output/$@.fs.tsv input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
 
 codingFillTest: mkdirs
-	${transMapPslToGenePred} -codingGapFillMax=13 input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -codingGapFillMax=13 -frameShifts=output/$@.fs.tsv input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
 
 fillTest: mkdirs
-	${transMapPslToGenePred} -nonCodingGapFillMax=20 -codingGapFillMax=10 input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -nonCodingGapFillMax=20 -codingGapFillMax=10 -frameShifts=output/$@.fs.tsv input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
 
 fill30Test: mkdirs
-	${transMapPslToGenePred} -nonCodingGapFillMax=30 -codingGapFillMax=30 input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -nonCodingGapFillMax=30 -codingGapFillMax=30 -frameShifts=output/$@.fs.tsv input/musstrain.src.gp input/musstrain.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
 
 # ENST00000625058.1 - two base genomic insertion in CDS
 # ENST00000486585.1 - incomplete CDS start and maps to opposite strand
 cds2InsertTest: mkdirs
-	${transMapPslToGenePred} -nonCodingGapFillMax=30 -codingGapFillMax=30 input/chimp.src.gp input/chimp.mapped.psl output/$@.mapped.gp
+	${transMapPslToGenePred} -nonCodingGapFillMax=30 -codingGapFillMax=30 -frameShifts=output/$@.fs.tsv input/chimp.src.gp input/chimp.mapped.psl output/$@.mapped.gp
 	genePredCheck -verbose=0 output/$@.mapped.gp
 	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
+
+# test cases from transmap V5 astMex1 to hg38
+tmAstMex1Tests: tmAstMex1NoMergeTests
+
+tmAstMex1NoMergeTests: mkdirs
+	${transMapPslToGenePred} -noBlockMerge -frameShifts=output/$@.fs.tsv input/tm-astMex1.ensembl.gp input/tm-astMex1-hg38.ensembl.psl output/$@.mapped.gp
+	genePredCheck -verbose=0 output/$@.mapped.gp
+	${diff} expected/$@.mapped.gp output/$@.mapped.gp
+	${diff} expected/$@.fs.tsv output/$@.fs.tsv
+
 
 clean::
 	rm -rf output
 
 mkdirs:
 	@${MKDIR} output