Included dimers, and left a commented line for equivalent SSR counts

svn path=/; revision=424

diff --git a/Personnel/preecej/perl_singletons/monococcum_ssr_mash.pl b/Personnel/preecej/perl_singletons/monococcum_ssr_mash.pl
index f5cece53c9f2173d936b9ddab86427cdbd829fcd..a8b5795a321493c18fc7d915a825a81cfc86d441 100644 (file)
--- a/Personnel/preecej/perl_singletons/monococcum_ssr_mash.pl
+++ b/Personnel/preecej/perl_singletons/monococcum_ssr_mash.pl
@@ -91,13 +91,14 @@ sub stitch_ssr_to_ortho()
                         if ($curr_DV_ssr_word eq $curr_G3_ssr_word) {
                             #print "$DV_locus:$curr_DV_ssr_word:" . $DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word}
                             #    . "\t$G3_locus:$curr_G3_ssr_word:" . $G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word} . "\n";
-                            if ($DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word} != $G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word}) 
+                            #if ($DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word} == $G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word}) # equivalent SSR counts 
+                            if ($DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word} != $G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word})  # differential SSR counts
                             {
-                                if ((length($curr_DV_ssr_word) > 2)) { # dimer exclusion
+                                #if ((length($curr_DV_ssr_word) > 2)) { # dimer exclusion
                                     print "$curr_DV_ssr_word"
                                         . "\t$DV_locus\t$DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word}"
                                         . "\t$G3_locus\t$G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word}\n";
-                                }
+                                #}
                                 #print "$DV_locus:$curr_DV_ssr_word:" . $DV{$DV_locus}{ssr_words}{$curr_DV_ssr_word}
                                 #    . "\t$G3_locus:$curr_G3_ssr_word:" . $G3{$G3_locus}{ssr_words}{$curr_G3_ssr_word} . "\n";
                             }