Account for the several ways to read variant files in htslib

[jmthibault79]

There are at least three ways to read variant files in htslib: indexed, unindexed, and synced. Each has advantages and drawbacks. Enable the use of all of these via Variant Reader/Iterators and make a record of when it's appropriate to use each.

Where multiple options are available, run benchmarks to determine which is best.

[jmthibault79]

Also make sure there are tests for all of the valid combinations.

[jmthibault79]

• VariantReader/Iterator uses htslib bcf_open and bcf_read1 to read a single file line by line.
• MultipleVariantReader/Iterator uses a priority queue of VariantIterators
• IndexedVariantReader/Iterator uses htslib bcf_open and bcf_itr_next to read a single indexed file over a set of intervals.
• SyncedVariantReader/Iterator uses htslib bcf_sr_add_reader and bcf_sr_next_line to read multiple indexed files over a set of intervals.

[jmthibault79]

	VariantReader	IndexedVR	MultipleVR	SyncedVR
VCF	YES	no	YES	no
VCF GZ	YES	no	YES	YES
BCF	YES	YES	YES	YES
Single	YES	YES	YES	YES
Multiple	no	no	YES	YES
Index	no	YES	no	YES
Interval	no	YES	no	YES
Requires Index	no	YES	no	YES
Requires Interval	no	no	no	no (#236)

[jmthibault79]

• One file, no index, no intervals, VCF/VCF.GZ/BCF: use VariantReader
• Multiple files, no index, no intervals, VCF/VCF.GZ/BCF: use MultipleVariantReader (or VariantReader with zip-iteration)
• One file, using index and intervals, BCF: use IndexedVariantReader or SyncedVariantReader (need to benchmark which is better)
• One file, using index and intervals, VCF.GZ: use SyncedVariantReader
• Multiple files, using index and intervals, VCF.GZ/BCF: use SyncedVariantReader

Missing functionality:

• Intervals with VCF files
• Intervals with unindexed files (related because htslib doesn't handle VCF indices)

Unknown/untested:

• BCF GZ / Compressed BCF files
• SyncedVariantReader with no intervals given

[jmthibault79]

SyncedVariantReader works with no intervals after #236

[MauricioCarneiro]

Added ticket #237 for the single indexed BCF question. Added ticket #239 for intervals with VCF files Added ticket #240 for Intervals with unindexed files (related because htslib doesn't handle VCF indices)

I would ignore BCF GZ, that's an abomination because BCF's can be intrinsically gzipped....