Release 1.105

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1630 8bce386e-0d6e-43e0-b1ca-608082c0432d
Conditionally allow for tabs in ped file fields


git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1633 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed bad 'equals' bug in VC validation where Integer != Integer was always returning true (duh)

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1634 8bce386e-0d6e-43e0-b1ca-608082c0432d
Move class net.sf.picard.util.Interval to net.sf.samtools.  I apologize to developers whose code will need to be modified to adapt to this change, but there was no easy way to make this change in a backward-compatible way.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1635 8bce386e-0d6e-43e0-b1ca-608082c0432d
Revert move of Interval.  It is now back in net.sf.picard.util.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1636 8bce386e-0d6e-43e0-b1ca-608082c0432d
Avoid asking for an array bigger than JVM allows if heap is huge.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1637 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed up docs for VC and Allele and added a method to remove a list of attributes for the VCBuilder.



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1638 8bce386e-0d6e-43e0-b1ca-608082c0432d
Adding better error message for unsupported VCF functionality



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1639 8bce386e-0d6e-43e0-b1ca-608082c0432d
Instead of failing badly on format field lists with '.'s, just ignore them.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1640 8bce386e-0d6e-43e0-b1ca-608082c0432d
Changed the iterator returned by getQuerynameSortedAlignedRecords() to return a header with SortOrder.queryname instead of coordinate.  Also added a warning log when SamAlignmentMerger decides it needs to re-sort the aligned reads into queryname order.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1641 8bce386e-0d6e-43e0-b1ca-608082c0432d
Add BCF encoding support for Java arrays, not just lists.



git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1642 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added ability to customize verb phrase used in progress logger.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1643 8bce386e-0d6e-43e0-b1ca-608082c0432d
Addeds support for processing reads with hard clips in MergeBamAlignment.  Implemented by transforming the hard clips to soft clips and adding in dummy bases and qualities when reading the aligned reads into memory.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1644 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fixed the handling of supplemental alignments.  Previous implementation was incorrect in assuming that when reads are paired that each end of a pair would have the same number of supplemental alignments.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1645 8bce386e-0d6e-43e0-b1ca-608082c0432d
Fix CleanSam to handle unusual Cigar strings, and also so that it no longer clips 1 more than necessary.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1646 8bce386e-0d6e-43e0-b1ca-608082c0432d
Eliminate order-dependence of test methods, and write test file to temp directory.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1647 8bce386e-0d6e-43e0-b1ca-608082c0432d
Write test output files into temp directory and clean them up on exit.
Eliminate IntelliJ yellow.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1648 8bce386e-0d6e-43e0-b1ca-608082c0432d
Treat SO:unknown as if it were SO:unsorted.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1649 8bce386e-0d6e-43e0-b1ca-608082c0432d
Added new SAMFileReader.query method that enables querying of multiple intervals in a single invocation.  In many cases this will be much more efficient than querying each interval separately, because due to the limitations of BAM index a query can result in many records read from the file that do not satisfy the query parameters.  In multiple query invocations, the same regions of the file may be read more than once, whereas with the new method each candidate region of the file will be read only once.

SamLocusIterator now uses this method.  It used to be the case that for some inputs, having SamLocusIterator use an index was less efficient than a linear scan through the whole file.  It should now be the case that using the index will always be at least as efficient as a linear scan, an generally using the index will be much more efficient.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1650 8bce386e-0d6e-43e0-b1ca-608082c0432d
Support .fna and .fna.gz as valid extensions for fasta files.

git-svn-id: http://svn.code.sf.net/p/picard/code/trunk@1651 8bce386e-0d6e-43e0-b1ca-608082c0432d