Merge branch 'develop' (htslib-1.10 support)

Breaking changes!

* 64-bit coordinates
* Revamped namespace
	- dhtslib.* represents helpers, idiomatic D, utils not in htslib
	- htslib.* represents direct C bindings
	- htslib top level module name [i.e., not dhtslib.htslib.*]
* SAM Header convenience structure (dhtslib.sam.header)

Unfortunately in the merge dhtslib.cigar and dhtslib.md which had Windows
line endings were replaced in their entirety so the diff may not show
what (if anything) changed.

Author: jblachly

dstep/Makefile

@@ -0,0 +1,26 @@
+
+DSTEP=dstep --space-after-function-name=false
+
+outputfiles=output/faidx.d output/kstring.d
+
+all: $(outputfiles)
+.PHONY: all
+
+vpath %.h include
+vpath %.diff patches
+
+$(outputfiles): output/%.d: %.h %.diff
+	$(DSTEP) $< -o /tmp/$(notdir $@)
+	patch /tmp/$(notdir $@) -o $@ < patches/$*.diff
+
+output/bgzf.d: /tmp/bgzf.d patches/bgzf.diff
+	patch /tmp/bgzf.d -o output/bgzf.d < patches/bgzf.diff
+
+/tmp/bgzf.d: include/bgzf.h
+	dstep include/bgzf.h -o /tmp/bgzf.d
+
+output/cram.d: /tmp/cram.d patches/cram.diff
+	$(DSTEP) -o /tmp/cram.d include/cram.h
+	patch /tmp/cram.d -o output/cram.d < patches/cram.diff
+
+

dstep/README

@@ -0,0 +1,14 @@
+Here we will use dstep (https://github.com/jacob-carlborg/dstep) to assist in
+conversion of htslib header files to D modules in the `htslib.*` namespace.
+
+Importantly, dstep does not get things 100% right (or when it does, we may
+prefer e.g. an inline function instead of a generic templated fn to replace
+a #define; or we may wish to add deprecated("...") etc.), and so we will store
+a patch for each (?) file to track any further transformation(s) before it can
+go in-tree. 
+
+This will also be critically important when upgrading the bindings to a new
+library version, so that we do not have to manually track fixes to the auto-
+mated conversion and can re-apply them (assuming `patch` can locate the hunk)
+
+Add new conversion to the Makefile

dstep/include

@@ -0,0 +1 @@
+../source/htslib/include-1.10/