drio

if(0 == output_count && 0 == no_output && NULL != output_prefix) 

drio

drio@milhouse:/mnt/slx/bfast_related/test.bwa.bf2.ecoli $ head test.txt 
Chr1    2       G       G       30      0       60      1       ^~.     E
Chr1    3       C       C       30      0       60      1       .       E
Chr1    4       T       T       30      0       60      1       .       E
Chr1    5       T       T       30      0       60      1       .       E
Chr1    6       T       T       30      0       60      1       .       E
Chr1    7       T       T       30      0       60      1       .       E
Chr1    8       C       C       30      0       60      1       .       E
Chr1    9       A       A       30      0       60      1       .       E
Chr1    10      T       T       33      0       60      2       .^~.    EE

drio

$ samtools flagstat 4.50.bam 
9823052 in total
0 QC failure
0 duplicates
3461351 mapped (35.24%)
9823052 paired in sequencing
9823052 read1
0 read2
9823052 properly paired (100.00%)
2200437 with itself and mate mapped

drio

drio@ned:/tmp **$ tar xfjO data.tar.bz2 tests.md5

drio

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

run()
{
  echo "`date`: $1"
  echo $1 | /bin/bash
  if [ $? -ne 0 ]

drio

#!/usr/bin/env ruby
#

=begin
  Pass a dir (output ?)
  Find all the txt
  Per each txt (tcpWindowSize.txt) 
  Create output/2007-07-25.title.html
    ---
    layout: post

drio

#!/usr/bin/env ruby
#
require 'find'
require 'fileutils'

i_dir = ARGV[0]
o_dir = "./output"

header = <<END
---

drio

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

dist=`pwd`
#fq="$dist/reads/ecoli.reads.fastq"
#fq="$dist/reads/reads.problem_zlib.fastq"
fq="$dist/reads/hybrid.fastq"
ref_h="/stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa"

drio

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

dist=`pwd`
#fq="$dist/reads/ecoli.reads.fastq"
#fq="$dist/reads/reads.problem_zlib.fastq"
fq="$dist/reads/hybrid.fastq"
ref_h="/stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa"

drio

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

#fq="$dist/reads/ecoli.reads.fastq"
#fq="$dist/reads/reads.problem_zlib.fastq"
fq="`pwd`/reads/hybrid.fastq"
ref_h="/stornext/snfs4/next-gen/solid/bf.references/h/hsap.36.1.hg18/hsap_36.1_hg18.fa"
ref_e="`pwd`/bfast.indexes/ecoli/ecoli.drio.test.fa"