Picard vs Samtools queryname sort incompatibility is a common user pain point

[clintval]

Picard/fgbio/htsjdk aligned files (such as to a wildtype genome) are of a different sort order to the often-used samtools approach of using samtools fastq and aligning with bwa. Thus this exception is hit when trying to neodisambiguate:

neodisambiguate/neodisambiguate/src/io/cvbio/neodisambiguate/bam/Bams.scala

Lines 68 to 73 in db7a512

	require(
	templates.map(_.name).distinct.length <= 1,
	"Templates with different names found! This can only occur if your SAM sources are queryname sorted using"
	+ " different implementations, such as with Picard tools versus Samtools. If you have encountered this"
	+ " exception, then please alert the maintainer!"
	)

It might be nice to have a fallback mode that re-sorts the SAM streams if they:

• Say they are queryname sorted
• And appear out of order (parsimony is different sort implementations)

[clintval]

Samtools as of at least 1.22.1 adds a sub-sort value:

@HD	VN:1.6	SO:queryname	SS:queryname:natural

But as of 3.4.0 Picard does not:

@HD	VN:1.6	SO:queryname	GO:query