feat: added sort macro to libn. moved macro based templates to more obvious directory

1 files changed, 12 insertions, 0 deletions

diff --git a/include/libbio.h b/include/libbio.h
index b405810..3db742d 100644
--- a/include/libbio.h
+++ b/include/libbio.h
@@ -31,6 +31,7 @@ error    bio·writenewick(bio·Tree tree, io·Putter out, void*);
 // -----------------------------------------------------------------------
 // Sequences
 
+/* i/o */
 typedef struct bio·FastaReader bio·FastaReader;
 typedef struct bio·FastqReader bio·FastqReader;
 
@@ -49,3 +50,14 @@ error            bio·closefasta(bio·FastaReader *rdr);
 bio·FastqReader *bio·openfastq(io·Reader stream, void *s, mem·Allocator heap, void *h);
 error            bio·readfastq(bio·FastqReader *rdr, bio·Seq *seq);
 error            bio·closefastq(bio·FastqReader *rdr);
+
+/* alignment */
+enum
+{
+    aln·K = 20,     // kmer size (k <= 32)
+    aln·L = 3,      // number of kmers / hash
+    aln·N = 1000,   // number of hashes
+};
+
+error aln·sketch(byte *seq, int l, uint64 *phi[aln·N], int *locs[aln·N]);
+error aln·sort(int len, int l, uint64 *vals);