-prefer_gain is removed

ncbi · May 31, 2021 · 77811df · 77811df
1 parent fd689b1
commit 77811df
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Showing 5 changed files with 13 additions and 6 deletions.
diff --git a/phylogeny/calibrateDissims.sh b/phylogeny/calibrateDissims.sh
@@ -31,7 +31,8 @@ LARGE_PAR=""
 if [ $LARGE -eq 1 ]; then
   LARGE_PAR="-large"
 fi
-$THIS/makeFeatureTree  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR  -prefer_gain  -nominal_singleton_is_optional  -qual $TMP.qual
+$THIS/makeFeatureTree  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  -qual $TMP.qual
+  # -prefer_gain  
 
 
 rm $TMP*  
diff --git a/phylogeny/tree2_quality_phen.sh b/phylogeny/tree2_quality_phen.sh
@@ -75,9 +75,11 @@ if [ $LARGE == 1 ]; then
 fi
 
 echo ""
-$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree1  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  -prefer_gain  -output_core $TMP.core1  -qual $TMP.qual1  -gain_nodes $TMP.gain_nodes1  -disagreement_nodes $TMP.disagreement_nodes1
+$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree1  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  -output_core $TMP.core1  -qual $TMP.qual1  -gain_nodes $TMP.gain_nodes1  -disagreement_nodes $TMP.disagreement_nodes1
+  # -prefer_gain  
 echo ""
-$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree2  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  -prefer_gain  -output_core $TMP.core2  -qual $TMP.qual2  -gain_nodes $TMP.gain_nodes2  -disagreement_nodes $TMP.disagreement_nodes2
+$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree2  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  -output_core $TMP.core2  -qual $TMP.qual2  -gain_nodes $TMP.gain_nodes2  -disagreement_nodes $TMP.disagreement_nodes2
+  # -prefer_gain  
 
 cat $TMP.qual1 | sed 's/ \([^1-9\(/+-]\)/_\1/g' > $TMP.qual1_
 cat $TMP.qual2 | sed 's/ \([^1-9\(/+-]\)/_\1/g' > $TMP.qual2_

diff --git a/phylogeny/tree2names.sh b/phylogeny/tree2names.sh
@@ -24,8 +24,9 @@ LARGE_PAR=""
 if [ $LARGE == 1 ]; then
   LARGE_PAR="-large"
 fi
-$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR  -prefer_gain  -save_mem \
+$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR    -save_mem \
   -qual qual  -gain_nodes gain_nodes  -disagreement_nodes disagreement_nodes
+  # -prefer_gain
 
 cut -f 1 disagreement_nodes | sort | uniq -c | sort -n -k 1 -r > disagreement_nodes.txt
 set +o errexit

diff --git a/phylogeny/tree_quality_phen.sh b/phylogeny/tree_quality_phen.sh
@@ -40,7 +40,8 @@ FIND_ROOT_PARAM=""
 if [ $FIND_ROOT == 1 ]; then
   FIND_ROOT_PARAM="-output_core $TMP.core  -save_mem"
 fi
-$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR  -prefer_gain  -nominal_singleton_is_optional  $FIND_ROOT_PARAM  -qual $TMP.qual
+$THIS/makeFeatureTree  -threads 15  -input_tree $TMP.feature_tree  -features $PHEN  $LARGE_PAR  -nominal_singleton_is_optional  $FIND_ROOT_PARAM  -qual $TMP.qual
+  # -prefer_gain  
 
 if [ "$QUAL" ]; then
   cp $TMP.qual $QUAL

diff --git a/version.inc b/version.inc
@@ -1,6 +1,8 @@
-#define VERSION "1.9.2"
+#define VERSION "1.9.3"
 
 
+// 1.9.3  05/30/2021  align.cpp: ambiguous aa J,U,O are replaced by X, selfScore is using X
+//                    -prefer_gain is removed
 // 1.9.2  05/18/2021  optimizeReinsert() invokes optimizeLargeSubgraphs(&changes)
 // 1.9.1  05/15/2021  inc/threads
 //                    distTree_inc_new.sh -reinsert does not process inc/new/