drio

#!/usr/bin/env ruby19
#
# Total time loading the reference genome: 0 hour, 3 minutes and 2 seconds.
# Total time loading and deleting indexes: 6 hour, 28 minutes and 36 seconds.
# Total time searching indexes: 1 hour, 30 minutes and 2 seconds.
# Total time merging and writing output: 0 hour, 12 minutes and 25 seconds.
# Total time elapsed: 8 hours, 20 minutes and 12 seconds.
#
require 'find'

drio

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

help()
{
  [ ".$1" != "." ] && echo "ERROR: $1"
  cat<<EOF
Usage:

drio

#!/bin/bash
#
set -e

mkdir ./output
cmd="./parse.rb > ./output/data.txt && ./plot.sh ./output/data.txt"
$cmd
#bsub -J bf.p.m -o log.out -e log.err $cmd

drio

warning: difference appears to be caused by prelink, adjusting expectations
Reading symbols from /lib64/libm.so.6...done.
Loaded symbols for /lib64/libm.so.6
Reading symbols from /usr/lib64/libz.so.1...done.
Loaded symbols for /usr/lib64/libz.so.1
Reading symbols from /usr/lib64/libbz2.so.1...done.
Loaded symbols for /usr/lib64/libbz2.so.1
Reading symbols from /lib64/libpthread.so.0...done.
Loaded symbols for /lib64/libpthread.so.0
Reading symbols from /lib64/libc.so.6...done.

drio

split -a 1 -d -l 400 bwa_25.single.fastq bwa_25only.fastq.

drio

Mon May 24 15:40:12 CDT 2010
-----------------------------

snfs5: 100 instances only

$ ./strace.monitor.sh 30 8383
29 --

2.004783

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bwa:427_67_118  0 chr10 74937431  0 23M * 0 0 CGCAAAAAAAAAAAAAAAAAAAA WN]VCAN[S#/][R=N]VSQW]] XT:A:R  CM:i:0  X0:i:477  XM:i:1  XO:i:0  XG:i:0  MD:Z:23

drio

#include <stdio.h>
#include <stdlib.h>
#include <string.h>

/*
Write a C routine with the following prototype:

  void condense_by_removing(
      char *z_terminated ,
      char char_to_remove

drio

$ cat plot_dist_mapq.rb 
#!/usr/bin/env ruby19
#
# time samtools view -F 4 ./0.bam | ./plot_dist_mapq.rb

h = Hash.new(0)
i = 0
STDIN.each do |l|
  $stderr.printf("\r%d", i) if i % 50000 == 0
  mq = l.split[4].to_i

drio

141     /*
  142     { 
  143       int t;
  144       char foo[52] = "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
  145       char bar[52] = "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
  146       char foo2[52]= "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
  147       char bar2[52]= "\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0\0";
  148       for(t=0;t<len;t++) { foo[t] = "01234"[seq[0][t]]; }
  149       for(t=0;t<len;t++) { bar[t] = "01234"[seq[1][t]]; }
  150       fprintf(stderr, " --> %s (%d) : [%s -- %s] \n", p->name , len, foo, bar);