From b1965fc69c3e33302a8733ac177b989aec0e4150 Mon Sep 17 00:00:00 2001
From: Vyacheslav Brover <vyacheslav.brover@nih.gov>
Date: Wed, 16 Oct 2024 20:50:34 -0400
Subject: [PATCH] #2: compute dissimilarity requests (0/1); #3: save old
 #1/dissim in #1/dissim.<version>.gz (0/1)

---
 phylogeny/distTree_inc_refresh_dissim.sh | 67 ++++++++++++++++--------
 1 file changed, 46 insertions(+), 21 deletions(-)

diff --git a/phylogeny/distTree_inc_refresh_dissim.sh b/phylogeny/distTree_inc_refresh_dissim.sh
index ab4f928b..194b2928 100755
--- a/phylogeny/distTree_inc_refresh_dissim.sh
+++ b/phylogeny/distTree_inc_refresh_dissim.sh
@@ -1,46 +1,71 @@
 #!/bin/bash --noprofile
-THIS=`dirname $0`
+THIS=$( dirname $0 )
 source $THIS/../bash_common.sh
-if [ $# -ne 1 ]; then
-  echo "Compute new #1/dissim given #1/tree; save old #1/dissim in #1/dissim.<version>"
+if [ $# -ne 3 ]; then
+  echo "Update #1/dissim"
   echo "#1: incremental distance tree directory"
+  echo "#2: compute dissimilarity requests (0/1)"
+  echo "#3: save old #1/dissim in #1/dissim.<version>.gz (0/1)"
   exit 1
 fi
 INC=$1
+REQ=$2
+SAVE=$3
 
 
-VER=`cat $INC/version`
+VER=$( cat $INC/version )
+THREADS=$( file2var $INC/threads 15 )
 
-N=15
-if [ -e $INC/threads ]; then
-  N=`cat $INC/threads`
-fi
-THREADS="-threads $N"
+
+wc -l $INC/dissim
 
 
-section "Saving $INC/dissim to $INC/dissim.$VER"
-if [ -e $INC/dissim.$VER ]; then
-  error "$INC/dissim.$VER exists"
+if [ $SAVE == 1 ]; then
+  section "Saving $INC/dissim to $INC/dissim.$VER"
+  if [ -e $INC/dissim.$VER ]; then
+    error "$INC/dissim.$VER exists"
+  fi
+  cp $INC/dissim $INC/dissim.$VER && gzip $INC/dissim.$VER &
 fi
-wc -l $INC/dissim
-cp $INC/dissim $INC/dissim.$VER
-gzip $INC/dissim.$VER &
 
 
-TMP=`mktemp`
+TMP=$( mktemp )
 comment $TMP
 
 
-section "Computing dissimilarity requests"
-$THIS/distTree_refresh_dissim $INC $TMP.req $INC/dissim $THREADS
 wc -l $INC/dissim
 
+if [ $REQ == 1 ]; then
+  section "Computing dissimilarity requests"
+  $THIS/distTree_refresh_dissim $INC $TMP.req $INC/dissim  -threads $THREADS
+else
+  cut -f 1,2 $INC/dissim > $TMP.req
+fi
+
 section "Computing dissimilarities"
 $THIS/distTree_inc_request2dissim.sh $INC $TMP.req $TMP.dissim-add
 
-section "Updating $INC/indiscern"
-$THIS/distTree_inc_dissim2indiscern.sh $INC $TMP.dissim-add
-cat $TMP.dissim-add >> $INC/dissim
+section "Updating $INC/dissim and $INC/indiscern"
+if [ $REQ == 1 ]; then
+  $THIS/distTree_inc_dissim2indiscern.sh $INC $TMP.dissim-add
+  cat $TMP.dissim-add >> $INC/dissim
+else
+  mv $TMP.dissim-add $INC/dissim
+  cp /dev/null $INC/indiscern
+  $THIS/distTree_inc_dissim2indiscern.sh $INC $INC/dissim
+  section "Updating $INC/tree"
+  cp $INC/tree $INC/hist/tree.$VER
+  gzip $INC/hist/tree.$VER
+  VARIANCE=$( cat $INC/variance )
+  $THIS/makeDistTree  -data $INC/  -output_tree $TMP.tree  -threads $THREADS  -variance $VARIANCE  -fix_discernible  -optimize  -skip_len  -subgraph_iter_max 2 > $INC/hist/makeDistTree.$VER
+  mv $TMP.tree $INC/tree
+fi
+
+section "QC $INC/indiscern"
+$THIS/distTree_inc_indiscern_qc.sh $INC 0 0
+
+VER=$(( VER + 1 ))
+echo $VER > $INC/version
 
 
 rm $TMP*