This page was last updated on Wednesday, 22-Jan-2014 16:11:26 CST

Installation notes for SAMStat version 1.09 7/7/2013

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Prerequisites

None

Installation

1. $ cd /programinstallers/
2. $ wget -N http://downloads.sourceforge.net/project/samstat/samstat.tgz
3. $ tar -zxvf samstat.tgz
4. $ cd samstat/src
5. Fix a bug in the program, file io.c line 265, change
   if(tmp == 4){
   to
   if(tmp & 4){
6. I also changed the source code to print out exact number of reads aligned
   File html_out.c line 1936
   

     fprintf(out,"<h2>Mapping stats: %0.0f%% aligned (%0.1fM aligned out of %0.1fM total) </h2>\n", mapped / total *100.0f,mapped  / 1000000.0f, total / 1000000.0f );

   changed to
   

     fprintf(out,"<h2>Mapping stats: %0.2f%% aligned (%0.1fM aligned (%0f) out of %0.1fM total (%0f)) </h2>\n", mapped / total *100.0f,mapped / 1000000.0f, mapped, total / 1000000.0f, total );

7. $ make
8. $ cp -puv samstat /usr/local/bin
9. Cleanup
   $ cd ../..
10. $ rm samstat -rf