Aiming to achieve Hadoop interoperability

This commit contains the ContextUtil class from Parquet that provides
some level of interoperability between different versions of Hadoop
to access Configuration objects. Thanks to Matt Massie for suggesting
this.
Aiming to achieve Hadoop interoperability

This commit contains the ContextUtil class from Parquet that provides
some level of interoperability between different versions of Hadoop
to access Configuration objects. Thanks to Matt Massie for suggesting
this.
Merge branch 'hadoop_interop' of ssh://git.code.sf.net/p/hadoop-bam/code into hadoop_interop
Adding treatment of RuntimeIOException to BAMSplitGuesser
BAMSplitGuesser: treatment of Picard exceptions

Some newer BAM files from 1000Genomes seem to cause issues for the
BAMSplitGuesser. This commit should fix the problem that caused
an incorrect offset for the start of a SAMRecord within the
uncompressed BGZF block. Also a debug mode that lists the split
point coordinates was added. For reference, one affected file was:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data/NA12878/high_coverage_alignment/NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam
Merge branch 'hadoop_interop'
Adding check for initialization to SAM and BAM RecordReaders
Merge remote-tracking branch: upstream/master