0.5

forest.sh

@@ -299,7 +299,7 @@ dcheck() {
   fi
   ## tac >8.0 ########################
   echo -e -n "> \e[1mtac\e[0m            >8.0       mandatory\t" ;    binexe=$TAC_BIN;
-  echo -e -n "$binexe    \t\t" ;
+  echo -e -n "$binexe     \t\t" ;
   if [ ! $(command -v $binexe) ]; then echo -e "\e[31m[fail]\e[0m";
   else        echo -e -n "$(which $binexe)\t\t\e[32m[ok]\e[0m\t\t";   $TAC_BIN --version | sed -n '1p;q' ;
   fi
@@ -543,7 +543,7 @@ then
 	      
   # selecting trees
   mv $FOREST $TMP ;
-  while IFS=$'\t' read -r llk tre
+  while read -r llk tre  # using IFS=$'\t' is slow...
   do
     chk=$($BAWK -v d=$DELTA '($1-$2<=d){print"OK"}' <<<"$BESTLK $llk");
     [ "$chk" == "OK" ] && echo -e "$llk\t$tre" >> $FOREST ;
@@ -572,7 +572,7 @@ else ############################## <=== option -t
 
   # checking no. sequences and leaves
   na=$(grep "^>" $ALN | wc -l);
-  while read t
+  while read -r t
   do
     nt=$(tr '(,' '\n' <<<"$t" | grep -c -v "^$");
     if [ $nt -ne $na ]
@@ -598,7 +598,7 @@ else ############################## <=== option -t
     tml="$(sed -n '1p;q' $MLTREE)";
     hml="$(hashtree $tml)";
     # discarding duplicate trees (if any)
-    while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $MLTREE |
+    while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $MLTREE |
       grep -v -F "$hml" |
         sort |
           $TAWK '($1==p){next} {p=$1;print$2}' > $TMP ;
@@ -643,7 +643,7 @@ else ############################## <=== option -t
     # adding other trees
     cat $TMP >> $INTREES ;
     # discarding duplicate trees (if any) and the ML one
-    while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $INTREES |
+    while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done < $INTREES |
       grep -v -F "$hml" |
         sort |
           $TAWK '($1==p){next} {p=$1;print$2}' > $TMP ;
@@ -671,7 +671,7 @@ else ############################## <=== option -t
   $BAWK '(NR==1){print$2}' $TMP> $MLTREE ;
 
   # selecting trees
-  while IFS=$'\t' read -r llk tre
+  while read -r llk tre  # using IFS=$'\t' is slow...
   do
     chk=$($BAWK -v d=$DELTA '($1-$2<=d){print"OK"}' <<<"$BESTLK $llk");
     [ "$chk" == "OK" ] && echo -e "$llk\t$tre" >> $FOREST ;
@@ -721,7 +721,7 @@ then
   
     # building neighborhoods
     cat $CURRENT | bash -c "$NEIGHBORHOOD" |
-      while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP ;
+      while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP ;
 
     # discarding already processed trees
     cat $TMP $HASHSET |
@@ -834,7 +834,7 @@ then
     
       # building neighborhoods
       cat $CURRENT.$t | bash -c "$NEIGHBORHOOD" |
-        while read tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP.$t &
+        while read -r tre ; do echo -e "$(hashtree $tre)\t$tre" ; done > $TMP.$t &
 
       t=$(( $t - 1 ));
     done