updated README

README.md

@@ -8,28 +8,56 @@ less code.
 
 ## Usage
 
-### Use cgranges as a library
+### Test with BED coveragae
+
+For testing purposes, this repo implements the [bedtools coverage][bedcov] tool
+with cgranges. The source code is located in the [test/](test) directory. You
+can compile and run the test with:
+```sh
+cd test && make
+./bedcov-cr test1.bed test2.bed
+```
+The first BED file is loaded into RAM and indexed. The depth and the breadth of
+coverage of each region in the second file is computed by query the index of
+the first file.
+
+The [test/](test) directory also contains a few other implementations based on
+[IntervalTree.h][ekg-itree] in C++, [quicksect][quicksect] in Cython and
+[ncls][ncls] in Cython.
+
+### Use cgranges as a C library
 
 ```c
-#include <stdio.h>
-#include <stdlib.h>
-#include "cgranges.h"
-
-int main(void)
-{
-	cgranges_t *cr = cr_init(); // initialize a cgranges_t object
-	cr_add(cr, "chr1", 20, 30, 0); // add a genomic interval
-	cr_add(cr, "chr2", 10, 30, 1);
-	cr_add(cr, "chr1", 10, 25, 2);
-	cr_index(cr); // index
-
-	int64_t i, n, *b = 0, max_b = 0;
-	n = cr_overlap(cr, "chr1", 15, 22, &b, &max_b); // overlap query; output array b[] can be reused
-	for (i = 0; i < n; ++i) // traverse overlapping intervals
-		printf("%d\t%d\t%d\n", cr_start(cr, b[i]), cr_end(cr, b[i]), cr_label(cr, b[i]));
-	free(b); // b[] is allocated by malloc() inside cr_overlap(), so needs to be freed with free()
-
-	cr_destroy(cr);
-	return 0;
-}
+cgranges_t *cr = cr_init(); // initialize a cgranges_t object
+cr_add(cr, "chr1", 20, 30, 0); // add a genomic interval
+cr_add(cr, "chr2", 10, 30, 1);
+cr_add(cr, "chr1", 10, 25, 2);
+cr_index(cr); // index
+
+int64_t i, n, *b = 0, max_b = 0;
+n = cr_overlap(cr, "chr1", 15, 22, &b, &max_b); // overlap query; output array b[] can be reused
+for (i = 0; i < n; ++i) // traverse overlapping intervals
+printf("%d\t%d\t%d\n", cr_start(cr, b[i]), cr_end(cr, b[i]), cr_label(cr, b[i]));
+free(b); // b[] is allocated by malloc() inside cr_overlap(), so needs to be freed with free()
+
+cr_destroy(cr);
 ```
+
+### Use IITree as a C++ library
+
+```cpp
+IITree<int, int> tree;
+tree.add(12, 34, 0); // add an interval
+tree.add(0, 23, 1);
+tree.add(34, 56, 2);
+tree.index(); // index
+std::vector<size_t> a;
+tree.overlap(22, 25, a); // retrieve overlaps
+for (size_t i = 0; i < a.size(); ++i)
+	printf("%d\t%d\t%d\n", tree.start(a[i]), tree.end(a[i]), tree.data(a[i]));
+```
+
+[bedcov]: https://bedtools.readthedocs.io/en/latest/content/tools/coverage.html
+[ekg-itree]: https://github.com/ekg/intervaltree
+[quicksect]: https://github.com/brentp/quicksect
+[ncls]: https://github.com/hunt-genes/ncls