Fix link error

[jts]

On my setup (Ubuntu 12.04, gcc 4.6.3) linking fails unless -lpthread is explicitly passed to the linker

[nh13]

Closing as no response to #4

[jts]

I did not open issue 4 but I should have looked at the issue list before sending the pull request. I'll send my version of samtools next week.

[nh13]

The git repo now uses samtools as a submodule, so make sure you use that feature when you update dwgsim.

[jts]

Cloning:

> git clone --recursive git://github.com/nh13/DWGSIM
Cloning into 'DWGSIM'...
remote: Counting objects: 569, done.
remote: Compressing objects: 100% (225/225), done.
remote: Total 569 (delta 362), reused 551 (delta 344)
Receiving objects: 100% (569/569), 136.26 KiB, done.
Resolving deltas: 100% (362/362), done.
Submodule 'samtools' (http://github.com/samtools/samtools.git) registered for path 'samtools'
Cloning into 'samtools'...
remote: Counting objects: 4017, done.
remote: Compressing objects: 100% (1953/1953), done.
remote: Total 4017 (delta 2253), reused 3789 (delta 2060)
Receiving objects: 100% (4017/4017), 3.64 MiB, done.
Resolving deltas: 100% (2253/2253), done.
Submodule path 'samtools': checked out '28391e5898804ce6b805016d8c676fdf61442eb3'

Building:

> make
[...]
gcc -g -Wall -O3  -o dwgsim_eval src/dwgsim_eval.o samtools/knetfile.o samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/bedidx.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/bam_cat.o -Lsamtools -lm -lz
samtools/bgzf.o: In function `bgzf_mt':
/home/jsimpson/work/scratch/DWGSIM/samtools/bgzf.c:445: undefined reference to `pthread_create'
samtools/bgzf.o: In function `mt_destroy':
/home/jsimpson/work/scratch/DWGSIM/samtools/bgzf.c:458: undefined reference to `pthread_join'
samtools/bam_sort.o: In function `sort_blocks':
/home/jsimpson/work/scratch/DWGSIM/samtools/bam_sort.c:421: undefined reference to `pthread_create'
/home/jsimpson/work/scratch/DWGSIM/samtools/bam_sort.c:423: undefined reference to `pthread_join'

Versions:

> gcc --version
gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3
Copyright (C) 2011 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

> lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.2 LTS
Release:    12.04
Codename:   precise
``