revert changes to metrics path
Warns potential index mismatch if chrom not found in realignment sequence dictionary (gives total count)
Merge remote-tracking branch 'upstream/master'

Conflicts:
	Socrates
	bin/net/wehi/socrates/AnnotatePairedClusters.class
	bin/net/wehi/socrates/BAMStratifier$AlignmentInfo.class
	bin/net/wehi/socrates/BAMStratifier$MergeWorker.class
	bin/net/wehi/socrates/BAMStratifier$OutputFiles.class
	bin/net/wehi/socrates/BAMStratifier$StratifyWorker.class
	bin/net/wehi/socrates/BAMStratifier.class
	bin/net/wehi/socrates/Cluster.class
	bin/net/wehi/socrates/PairedCluster.class
	bin/net/wehi/socrates/RealignmentBAM$Info.class
	bin/net/wehi/socrates/RealignmentBAM.class
	bin/net/wehi/socrates/RealignmentClustering$ClusteringWorker.class
	bin/net/wehi/socrates/RealignmentClustering$ResultCounter.class
	bin/net/wehi/socrates/RealignmentClustering.class
	bin/net/wehi/socrates/SOCRATES.class
	bin/net/wehi/socrates/util/ConsensusMaker.class
	bin/net/wehi/socrates/util/FindSeqByName.class
	bin/net/wehi/socrates/util/GenomicIndexInterval.class
	bin/net/wehi/socrates/util/GenomicIntervalList.class
	bin/net/wehi/socrates/util/GenomicIntervalListMap.class
	bin/net/wehi/socrates/util/MemoryMappedFile.class
	bin/net/wehi/socrates/util/ProgressVerbose.class
	bin/net/wehi/socrates/util/RealignmentCluster.class
	bin/net/wehi/socrates/util/RealignmentRecordSummary.class
	bin/net/wehi/socrates/util/SAMFileInfo.class
	bin/net/wehi/socrates/util/SAMRecordSummary.class
	bin/net/wehi/socrates/util/SeekableMemoryStream.class
	bin/net/wehi/socrates/util/TabixReader$Iterator.class
	bin/net/wehi/socrates/util/TabixReader$TIndex.class
	bin/net/wehi/socrates/util/TabixReader$TIntv.class
	bin/net/wehi/socrates/util/TabixReader$TPair64.class
	bin/net/wehi/socrates/util/TabixReader.class
	bin/net/wehi/socrates/util/Utilities.class
	bin/net/wehi/socrates/util/Values.class
	src/net/wehi/socrates/RealignmentBAM.java