Synchronize on the 'out' PrintStream instead of 'this' to avoid mixing
up log statements from different threads. Example from actual log file:

DEBUG	DEBUG	2014-06-02 08:48:46	IlluminaBasecallsConverter	Reading data
from tile 11206 ...
2014-06-02 08:48:46	IlluminaDataProviderFactory	The following parsers
will be used by IlluminaDataProvider:
Add additional boolean genotype functions to JEXLMap to add functionality to GATK tools using JEXL (like VariantFiltration)
Merge pull request #32 from samtools/ldg_newJEXLmapGTs

Add additional boolean genotype functions to JEXLMap to add functionalit...
Bug fix in `RelativeIso8601Date`: non-lazy times are not deserialized properly.
FastqRecord: added methods equals, hashcode, toString, length
Merge pull request #37 from lindenb/fastq2

FastqRecord: added methods equals, hashcode, toString, length
Merge pull request #36 from samtools/mm_bugfix_isodate

Bug fix in `RelativeIso8601Date`: non-lazy times are not deserialized properly.
Add some logging to particularly long-running method.
Merge pull request #38 from samtools/mm_logging

Add some logging to particularly long-running method.
Use the same buffer as the rest of htslib
Merge pull request #41 from lletourn/defaultBuffer

Use the same buffer as the rest of htslib in the reference sequence / fasta file classes.
When querying for a contig which doesn't exist in SAMFileReader, return an empty iterator. This matches the behavior in BAMFileReader
Use a StringBuffer instead of synchronization when generating log
messages. The only exception is if the stacktrace of a Throwable also
needs to be written. Then we have to ensure that our message goes with
the stacktrace so we need synchronization there. But this should not be
a drawback since the Throwable.printStackTrace() itself synchronizes on
the PrintStream.
Merge pull request #30 from nnordborg/synchronize-log

The logging implementation is not thread-safe
Release 1.115
adding travis-ci
Merge pull request #45 from samtools/nh_travis_ci

adding travis-ci
adding build status in the README
Merge pull request #47 from samtools/nh_readme_with_build_status

adding build status in the README
Checks if ReferenceFile is indexed, and if so, uses it

added tests.