Case of symbolic allele ID string now being preserved as per VCFv4.1 section 1.4.5
When querying for a contig which doesn't exist in SAMFileReader, return an empty iterator. This matches the behavior in BAMFileReader
Update TabixReader.java
Explicitly implementing Closeable on classes and interfaces with a void close() definition
Fix signature of CloserUtil.close(List) so that is it more likely to be invoked.
Merge pull request #61 from samtools/aw_fix_closer_util

Fix signature of CloserUtil.close(List) so that is it more likely to be ...
Merge branch 'master' of https://github.com/d-cameron/htsjdk
Update TabixFeatureReader.java

Fix problem with open TabixReader after calling close() on the TabixFeatureReader
Merge pull request #65 from mremmert/patch-1

Correctly close underlying reader
Merge pull request #42 from jsilter/allow_empty_sam

Allow querying from contig which is not in file
Merge pull request #52 from marc-flesch/patch-1

Update TabixReader.java
Add constructor in VCFFileReader that allows to specify the index resource
constructor for fastqReader
FastqReader: added constructor, toString, removed extra-line
Fixed race condition where synchronouslyClose() would be called multiple
times if AbstractAsyncWriter.close() called twice simultaneously.
Allowing close() to be called multiple times as per java.io.Closeable
interface specifications.
Update TribbleIndexedFeatureReader.java, TabixReader.java, and
TabixFeatureReader.java to add new constructor with given index file.
Update AbstractFeatureReader.java to pass
index file forward to specific readers. Pass index file in AbstractFeatureReader
to underlying readers.
Merge pull request #66 from mremmert/issue54

Add constructor in VCFFileReader that allows to specify the index resour...
Merge pull request #67 from lindenb/fastqreader_cstor

constructor for fastqReader
Merge pull request #68 from samtools/closeable

Fixed race condition where synchronouslyClose() would be called multiple
Merge pull request #69 from samtools/pull_62

Update TribbleIndexedFeatureReader.java, TabixReader.java, and