Remove non-ascii character from comment
Make run_all.sh exit with non-zero in case of any integration test failures
(Hopefull) fix compatibility issue with Hadoop 1.x and Hadoop 2.0

Hadoop 2 changed the TaskAttemptContext from a class to an interface,
breaking our code.  Therefore, we need to instantiate a difference class
for TaskAttemptContext depending on the version of Hadoop.  Wanting to
maintain compatibility with both versions of Hadoop, this commit reworks the
code to use reflection to try both known options and use the first one
that works.

Conflicts:

	src/it/crs4/seal/tsv_sort/TextSampler.java
Document dependency on build-essential
In CutString, don't keep a reference to the original record

This commit also removes the explicit check against trying to access
fields before a String was loaded. We try to mitigate this risk by
returning null in such cases.
In CutText, don't keep a reference to the original record

This commit also removes the explicit check against trying to access
fields before a Text is loaded. We try to mitigate this risk by
returning null in such cases.
Apply reflection-based Hadoop 2 API compatibility fix to unit tests

A previous commit had dealt with the TaskAttemptContext change in the
Hadoop API within the TextSampler, which used to try to instantiate it
directly.  This commit refactors that code into a utility function (in
the Utils module) and uses it to fix some unit tests which presented the
same problem.
Fix bad sam record in unit test
From SamInputFormat, don't return objects that reference volatile data

This commit changes SamInputFormat and TextSamMapping so that they don't
return/contain objects that will be changed upon reading the next input
record.  Hadoop 2 seems to have optimized some input-related code
(probably LineRecordReader) to re-use its internal buffers.  Previously
TextSamMapping would optimistically keep a reference to the original
input Text object; with Hadoop 2, this object is getting wiped as the
next record is read. With this commit all necessary data is copied into
the object.
Remove seal.lib.hadut

The hadut module has been superceded by pydoop.hadut and other modules
provided by pydoop.  It only presents a liability and would need to be
updated to work with Hadoop 2
Remove unused imports
Bring back seal.lib.hadut, in light form

The hadoop utilities module in Pydoop does not provide the functionality
for an easy migration.  This commit bring back the seal.lib.hadut module
but without the redundant functionality.
Use logger properly
initial commit of dist bcl2qseq
copy missing module to interpret illumina run directory meta-data
Rename dist_bcl2qseq.py  to seal_dist_bcl2convert
Use standard logformat string in seal module
Remove module mechanism

The use of "module load" to enable bclToQseq for the tasks has been
replaced by a new parameter to add elements to LD_LIBRARY_PATH.  This
should make the program more generally usable, even in clusters that
don't use the module system.
Add 2 contributors
Don't include empty strings as arguments

The previous code generated the command as a string, so blanks were eaten up.
The new implementation executes the bclToQseq command directly, so blanks are
passed to it and result in an error.