From: Michael R. Crusoe <crusoe@debian.org>
Subject: Implement genomeSAindexNbases
Forwarded: https://github.com/trinityrnaseq/trinityrnaseq/issues/905#issuecomment-707094332
--- trinityrnaseq.orig/util/misc/run_STAR_via_samples_file.pl
+++ trinityrnaseq/util/misc/run_STAR_via_samples_file.pl
@@ -88,6 +88,7 @@
     }
 
     my $genomeChrBinNbits = min(18, int(log((-s $genome) / $num_contigs) / log(2) + 0.5) );
+    my $genomeSAindexNbases = int(log(-s $genome) / log(2) / 2) - 1;
     
     my @read_sets = &parse_samples_file($samples_file);    
 
@@ -102,6 +103,7 @@
     my $cmd = "$star_prog --runThreadN $CPU --runMode genomeGenerate --genomeDir $star_index "
         . " --genomeFastaFiles $genome "
         . " --genomeChrBinNbits $genomeChrBinNbits "
+        . " --genomeSAindexNbases $genomeSAindexNbases "
         . " --limitGenomeGenerateRAM 40419136213 ";
         
     if ($gtf_file) {
