Updated manuals and added new figures

eead-csic-compbio · May 4, 2016 · 865f311 · 865f311
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diff --git a/.gitignore b/.gitignore
@@ -3,3 +3,4 @@
 .RData
 README.html
 get_homologues.Rproj
+HOWTOmanuals
diff --git a/CHANGES.txt b/CHANGES.txt
@@ -122,3 +122,8 @@
 14042016: added option -c to plot_matrix_heatmap.sh to filter out excessive redundancy by imposing a max identity cut-off value
 28042016: updated manuals for the web
 29042016: updated manuals 
+04052016: set $MIN_PERSEQID_HOM_EST=70 and $MIN_COVERAGE_HOM_EST=50 in lib/marfil_homology.pm 
+04052016: added figure 3 to manual_get_homologues-est.pdf
+04052016: commented out debug print in marfil_homology::makeHomolog
+04052016: fixed bug in get_homologues-est.pl -c so that redundant isoforms are not added to pan/core sets
+04052016: fixed bug in get_homologues.pl -c so that inparalogues are substracted while adding up novel BDBH pan-genome genes
diff --git a/manual_get_homologues-est.pdf b/manual_get_homologues-est.pdf
diff --git a/manual_get_homologues.pdf b/manual_get_homologues.pdf
diff --git a/plot_pancore_matrix.pl b/plot_pancore_matrix.pl
@@ -384,7 +384,6 @@ sub plot_core_genome
   }
   else
   {
-
     open(RSHELL,"|R --no-save $Rparams ") || die "# plot_core_genome : cannot call R: $!\n";
     print RSHELL<<EOF;
-Original file line number
+Diff line change
@@ Expand Up / @@ -384,7 +384,6 @@ sub plot_core_genome @@
       }
       else
       {
         open(RSHELL,"|R --no-save $Rparams ") || die "# plot_core_genome : cannot call R: $!\n";
         print RSHELL<<EOF;
@@ Expand Down @@