The motivation for these changes is to speed up reading of VCFs, which use a slower custom line-reading class.  In order to use a different reader, it was necessary to make some changes to the the FeatureCodec API.

FeatureCodec had a tight coupling with PositionalBufferedStream, which was good and bad: it allowed the codec to query the position of the underlying stream at any time (necessary for indexing), but it also introduced a level of statefulness that prevented some optimizations.  Such optimizations might involve reading ahead in the stream (e.g., async reading), or using a different type of InputStream entirely.

With that in mind, I made the following changes to tribble:
* Abstract out FeatureCodec's dependency on PositionalBufferedStream, and instead have it depend upon any generic source class (such as a LineIterator).
* Make FeatureCodec capable of generating such a source given a generic InputStream. For the purposes of indexing, make FeatureCodec capable of generating an indexible source (see LocationAware), as well.  This latter source is likely slower than the non-indexible one, which is why it is generated via a different mechanism.
* Implementations for all the above API changes, especially in the area of AsciiFeatureCodec and using faster line readers.
* Some cleanup and generics-typing, while I was at it.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1525 8bce386e-0d6e-43e0-b1ca-608082c0432d
Remove unused IOUtil.java

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1526 8bce386e-0d6e-43e0-b1ca-608082c0432d
Don't read the header twice when using a WFIterator (in outer class constructor and then again in WFIterator); instead, skip the header when generating the PBS for the WFIterator.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1527 8bce386e-0d6e-43e0-b1ca-608082c0432d
Simplify documentation, and modify to make consistent with method-level documentation.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1528 8bce386e-0d6e-43e0-b1ca-608082c0432d
svn ignore intellij output directories.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1529 8bce386e-0d6e-43e0-b1ca-608082c0432d
Force compiler to use Java 6 bootclasspath even if JAVA_HOME is Java 7.  In order to do this, either the environment variable JAVA6_HOME must point to Java 6 JAVA_HOME, or -Djava6.home=<path> must be put on the ant command line.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1530 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed DelimitedTextFileWithHeaderParser to DelimitedTextFileWithHeaderIterator, which involved changing it from being an Iterable to an Iterator

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1531 8bce386e-0d6e-43e0-b1ca-608082c0432d
Tied to #1531, managed to not include these files

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1532 8bce386e-0d6e-43e0-b1ca-608082c0432d
When generating a site-only VCF, do not regenerate the alleles based on the subsetted genotypes.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1533 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix story 52571227: 
- make sure that only FORMAT, INFO and FILTER header lines will be added to the dictionary
- added unittest to test BCF2Utils.makeDictionary 
- remove some unused parameters from few constructors in VCFSimpleHeaderLine.  


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1534 8bce386e-0d6e-43e0-b1ca-608082c0432d
Slight wording change in comment

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1535 8bce386e-0d6e-43e0-b1ca-608082c0432d
Revert: Slight wording change in comment

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1536 8bce386e-0d6e-43e0-b1ca-608082c0432d
Moving MarkIlluminaAdapters from picard private to picard public

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1537 8bce386e-0d6e-43e0-b1ca-608082c0432d
Release 1.97

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1538 8bce386e-0d6e-43e0-b1ca-608082c0432d
Clarify that optimization is done instead of applying default regex.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1541 8bce386e-0d6e-43e0-b1ca-608082c0432d
Clarify that read name regex must match entire read name.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1542 8bce386e-0d6e-43e0-b1ca-608082c0432d
added predicted insert size optional option and removed unused import


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1543 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add methods for executing a command, interleaving stdout and stderr, and return exit status in addition to command output.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1544 8bce386e-0d6e-43e0-b1ca-608082c0432d