fix missing symlink and update workflow to handle diploid graphaligne…

…r output and fix error checking

.github/workflows/makefile.yml

@@ -79,8 +79,9 @@ jobs:
         echo >> mbg.sh 'xz -dc ../../cache/paths.gaf.xz          > paths.gaf'
 
         echo  > ga.sh '#!/bin/sh'
-        echo >> ga.sh 'if [ ! -e "graph" ] ; then'
-        echo >> ga.sh '  touch graph'
+        echo >> ga.sh 'if [ ! -e "graph.index" ] ; then'
+        echo >> ga.sh '  touch graph.index'
+        echo >> ga.sh '  touch diploid.index'
         echo >> ga.sh '  touch empty.gaf'
         echo >> ga.sh 'else'
         echo >> ga.sh '  xz -dc ../../cache/aligned001.WORKING.gaf.xz > aligned001.WORKING.gaf'
@@ -99,4 +100,7 @@ jobs:
         chmod 755 ga.sh
         chmod 755 lib/verkko/bin/utgcns
 
-        ./bin/verkko -d asm --no-correction --mbg $PWD/mbg.sh --graphaligner $PWD/ga.sh --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz || reportLogs
+        ./bin/verkko -d asm --no-correction --mbg $PWD/mbg.sh --graphaligner $PWD/ga.sh --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz
+        if [ ! -s asm/assembly.fasta ]; then
+           reportLogs
+        fi

src/Makefile

@@ -66,9 +66,6 @@ endif
 ifeq ($(wildcard overlapErrorAdjustment/findErrors.C), )
   $(shell ln -s canu/src/overlapErrorAdjustment overlapErrorAdjustment)
 endif
-ifeq ($(wildcard overlapInCore/overlapImport.C), )
-  $(shell ln -s canu/src/overlapInCore overlapInCore)
-endif
 ifeq ($(wildcard seqrequester/src), )
   $(shell ln -s canu/src/seqrequester seqrequester)
 endif
@@ -81,7 +78,10 @@ endif
 ifeq ($(wildcard utility/src), )
   $(shell ln -s canu/src/utility utility)
 endif
-ifeq ($(wildcard stores/sqStoreDumpFASTQ.C), )
+ifeq ($(wildcard overlapInCore/overlapImport.C), )
+  $(shell ln -s canu/src/overlapInCore)
+endif
+ifeq ($(wildcard overlapBasedTrimming/clearRangeFile.H), )
   $(shell ln -s canu/src/overlapBasedTrimming overlapBasedTrimming)
 endif
 
@@ -811,7 +811,7 @@ all: $(addprefix ${TARGET_DIR}/,${ALL_TGTS}) \
      ../lib/verkko/profiles/jobscript.sh \
      ../lib/verkko/profiles/slurm-sge-status.sh \
      ../lib/verkko/profiles/slurm-sge-submit.sh
-	@rm  -f gfa meryl overlapErrorAdjustment overlapBasedTrimming overlapInCore seqrequester stores utgcns utility
+	@rm  -f gfa meryl overlapInCore overlapErrorAdjustment overlapBasedTrimming seqrequester stores utgcns utility
 	@echo ""
 	@echo "Success!"
 	@echo "${MODULE} installed in ${TARGET_DIR}/bin/${MODULE}"
@@ -839,7 +839,7 @@ $(foreach TGT,${ALL_TGTS},\
   $(eval $(call ADD_CLEAN_RULE,${TGT})))
 clean:
 	rm -rf rukki/target
-	rm  -f gfa meryl overlapErrorAdjustment seqrequester stores utgcns utility
+	rm  -f gfa meryl overlapInCore overlapErrorAdjustment overlapBasedTrimming seqrequester stores utgcns utility
 	find build -type d -print | sort -r | xargs -n 100 rmdir
 
 deinstall:

src/main.mk

@@ -111,6 +111,8 @@ SOURCES      := utility/src/align/align-ksw2-driver.C \
                 \
                 stores/objectStore.C \
                 \
+                overlapInCore/liboverlap/Binomial_Bound.C \
+                \
                 utgcns/libpbutgcns/AlnGraphBoost.C  \
                 \
                 gfa/gfa.C \