From c0a7b53baf2a6e7bf9bc1fbec7ac05e43ac59154 Mon Sep 17 00:00:00 2001
From: Nicholas Noll <nbnoll@eml.cc>
Date: Wed, 8 Sep 2021 15:51:40 -0700
Subject: checkin

---
 include/libbio.h | 19 +++++++++----------
 include/libn.h   | 39 +++++++++++++++++++--------------------
 2 files changed, 28 insertions(+), 30 deletions(-)

(limited to 'include')

diff --git a/include/libbio.h b/include/libbio.h
index 558c163..b3d0426 100644
--- a/include/libbio.h
+++ b/include/libbio.h
@@ -5,15 +5,12 @@
 
 typedef struct bio·Node
 {
-    string name;
-    string comment;
-    double dist;
-    double support;
-    int    nnode;
-    int    nchild;
-    struct bio·Node *parent;
-    struct bio·Node *sibling;
-    struct bio·Node *child;
+    string name, comment;
+    double dist, support;
+    int    nnode, nchild;
+    struct bio·Node *parent, *sibling, *child;
+
+    void  *data;
 } bio·Node;
 
 typedef struct bio·Tree
@@ -53,7 +50,6 @@ error  bio·writenewick(bio·Tree tree, io·Putter out, void*);
 
 /* i/o */
 typedef struct bio·SeqReader bio·SeqReader;
-typedef struct bio·SeqWriter bio·SeqWriter;
 
 typedef struct bio·Seq
 {
@@ -68,3 +64,6 @@ error          bio·closeseq(bio·SeqReader *rdr);
 
 error          bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq);
 error          bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq);
+
+error          bio·writefasta(io·Writer io, void *wtr, bio·Seq seq);
+error          bio·writefastq(io·Writer io, void *wtr, bio·Seq seq);
diff --git a/include/libn.h b/include/libn.h
index 2b8dc4c..5d557ce 100644
--- a/include/libn.h
+++ b/include/libn.h
@@ -22,34 +22,31 @@ typedef wchar_t wchar;
 // ----------------------------------------------------------------------------
 // dynamic array
 
-typedef struct bufHdr
+typedef struct BufHdr
 {
     vlong len;
     vlong cap;
     byte  buf[];
-} bufHdr;
+} BufHdr;
 
-#define _bufHdr(s) ((bufHdr*)((uint8*)(s)-offsetof(bufHdr, buf)))
-#define buflen(s) ((s) ? (_bufHdr(s)->len) : 0)
-#define bufcap(s) ((s) ? (_bufHdr(s)->cap) : 0)
-#define bufend(s) ((s) + buflen(s))
-#define bufsize(s) ((s) ? (buflen(s) * sizeof((s)[0])) : 0)
+#define bufhdr(b)        ((BufHdr*)((uint8*)(b)-offsetof(BufHdr, buf)))
+#define buflen(b)        ((b) ? (bufhdr(b)->len) : 0)
+#define bufcap(b)        ((b) ? (bufhdr(b)->cap) : 0)
+#define bufend(b)        ((b) + buflen(b))
+#define bufsize(b)       ((b) ? (buflen(b) * sizeof((b)[0])) : 0)
 
-#define buffree(s) ((s) ? (free(_bufHdr(s)), (s) = nil) : 0)
-#define buffit(s, n) ((n) <= bufcap(s) ? 0 : ((s) = bufgrow((s), (n), sizeof(*(s)))))
+#define buffree(b)       ((b) ? (free(bufhdr(b)), (b) = nil) : 0)
+#define buffit(b, n)     ((n) <= bufcap(b) ? 0 : ((b) = ·bufgrow((b), (n), sizeof(*(b)))))
 
-#define bufresize(s, n)                                                        \
-    do {                                                                       \
-        (buffit(s, n));                                                        \
-        ((_bufHdr(s)->len) = (n));                                             \
-    } while (0)
+#define bufpush(b, ...)  (buffit((b), 1 + buflen(b)), (b)[bufhdr(b)->len++] = (__VA_ARGS__))
+#define bufaddn(b, n)    (buffit(b, buflen(b)+n), bufhdr(b)->len += n, b+bufhdr(b)->len-n)
 
-#define bufpush(s, ...) (buffit((s), 1 + buflen(s)), (s)[_bufHdr(s)->len++] = (__VA_ARGS__))
+#define bufpop(b)         ((b)[--bufhdr(b)->len])
+#define bufdel(b, i)      bufdeln((b), (i), 1)
+#define bufdeln(b, i, n)  (memmove((b)+(i), (b)+(i)+(n), sizeof(*(b))*(bufhdr(b)->len-(n)-(i)), bufhdr(b)->len -= (n))
+#define bufdelswap(b, i)  ((b)[i] = bufend(b)[-1], bufhdr(b)->len-=1)
 
-#define bufpop(s, i) (_bufpop((s), (i), sizeof(*(s))), (s)[_bufHdr(s)->len])
-
-void* bufgrow(void*, vlong, vlong);
-void _bufpop(void*, int, vlong);
+void* ·bufgrow(void*, vlong, vlong);
 
 // -----------------------------------------------------------------------------
 // memory allocation
@@ -408,9 +405,11 @@ void sort·strings(uintptr n, byte* arr[]);
 // fast random number generation
 
 error  rng·init(uint64 seed);
-double rng·random();
+double rng·random(void);
+double rng·exponential(double lambda);
 bool   rng·bernoulli(double f);
 uint64 rng·randi(int max);
+uint64 rng·poisson(double mean);
 
 // -----------------------------------------------------------------------------
 // variable arguments
-- 
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