drio

-rw-r--r-- 1 deiros next-gen 690M Jul 27 17:11 50.bmf
-rw-r--r-- 1 deiros next-gen 218M Jul 28 10:03 bwa.25.bmf

drio

$ /stornext/snfs1/next-gen/drio-scratch/drd.bio.toolbox/bam.stats.sh -i ./merged.sort.dups.bam -e 2
n_ends       : 2
min map qual : 0
BAM file detected
Waiting for samtools instances to complete ...
# Total  reads:  176373414

# Total  read1:  88186707
# mapped read1:  16062200 (18.21%)
# dups   read1:  282601 (.32%)

drio

*$ cat .tmux.conf 
set -g prefix C-w
unbind C-b
bind C-w send-prefix

bind s split-window -v
bind v split-window -h

bind < resize-pane -L 1
bind > resize-pane -R 1

drio

NOTE: I am using bash for this.

NOTE2: Another approach for getting tmux would be to use gentoo-prefix or netbsd's pkgsrc. I 
didn't have too much luck with gentoo-prefix. NetBSD was pretty straight forward but it had
an old version of tmux (1.1).

Here is how to get tmux compiled if you can get your systadmins to installed it ... or
any other weird reason. I assume you have some basic libraries and headers installed (like
ncurses, etc...). If not, you'll have to compile those ones too.

drio

#!/bin/sh
#
#set -e

check_requirements()
{
  [ ! -f $s2f_bin ] && error "bfast solid2fastq not found." 
  [ ! -f $bwa_s2f ] && error "bwa solid2fastq not found." 
  [ ! -x $s2f_bin ] && error "bfast solid2fastq not executable." 
  [ ! -x $bwa_s2f ] && error "bwa solid2fastq not exectutable." 

drio

#!/bin/sh
#
set -e

check_requirements()
{
  [ ! -f $s2f_bin ] && error "bfast solid2fastq not found." 
  [ ! -f $bwa_s2f ] && error "bwa solid2fastq not found." 
  [ ! -x $s2f_bin ] && error "bfast solid2fastq not executable." 
  [ ! -x $bwa_s2f ] && error "bwa solid2fastq not exectutable." 

drio

#!/bin/sh
#
set -e
set -x

check_requirements()
{
  [ ! -f $s2f_bin ] && error "bfast solid2fastq not found." 
  [ ! -f $bwa_s2f ] && error "bwa solid2fastq not found." 
  [ ! -x $s2f_bin ] && error "bfast solid2fastq not executable." 

drio

#!/bin/bash

(
echo "set t png"
echo "set size 0.5,1"
#echo "set xrange [0:0.1]"
echo "set yrange [0:1]"
echo plot \"-\" using 2:1 notitle with lines
cat bwa.dwgsim_eval.output.txt | awk '{print $5/$6" "($6-$5)/$6}'
) \

drio

 sudo diskutil unmount force /Users/drio/sshfs/ardmore 

drio

<colors>
<<include etc/colors.conf>>
</colors>

<fonts>
<<include etc/fonts.conf>>
</fonts>

<<include ideogram.conf>>