feat: updated fasta code to allow for iteration

2 files changed, 32 insertions, 8 deletions

diff --git a/include/libbio.h b/include/libbio.h
index 2dc3d45..4c93656 100644
--- a/include/libbio.h
+++ b/include/libbio.h
@@ -31,11 +31,14 @@ error    bio·writenewick(bio·Tree tree, io·Putter out, void*);
 // -----------------------------------------------------------------------
 // Sequences
 
-#if 0
 typedef struct bio·FastaReader bio·FastaReader;
-
-/* fasta/q i/o */
-bio·Seq *bio·newfastareader(Stream *file, mem·Allocator heap);
-bio·Seq *bio·readfasta(bio·FastaParser *p);
-error    bio·writefasta(bio·Seq *seq, Stream *out);
-#endif
+typedef struct bio·Seq
+{
+    int  len;
+    byte *name;
+    byte *s;
+    byte *q;
+} bio·Seq;
+
+bio·FastaReader *bio·newfastareader(io·Reader stream, void *s, mem·Allocator heap, void *h);
+error            bio·readfasta(bio·FastaReader *rdr, bio·Seq *seq);
diff --git a/include/libn.h b/include/libn.h
index 43600c0..99e4fdb 100644
--- a/include/libn.h
+++ b/include/libn.h
@@ -113,6 +113,8 @@ error   coro·free(Coro *c);
 // I/O
 
 typedef FILE Stream;
+typedef struct stat io·Stat;
+
 enum SeekPos
 {
     seek·CUR = SEEK_CUR,
@@ -121,11 +123,13 @@ enum SeekPos
 };
 
 Stream *io·open(byte *name, byte *mode);
+int     io·fd(Stream *s);
+error   io·stat(Stream *s, io·Stat *buf);
 error   io·close(Stream *s);
 byte    io·getbyte(Stream *s);
 error   io·ungetbyte(Stream *s, byte c);
 int     io·read(Stream *s, int sz, int n, void *buf);
-int     io·readln(Stream *s, int n, byte* buf);
+int     io·readln(Stream *s, int n, byte *buf);
 error   io·putbyte(Stream *s, byte c);
 int     io·putstring(Stream *s, string str);
 int     io·write(Stream *s, int sz, int n, void *buf);
@@ -139,6 +143,11 @@ typedef struct io·Reader
     int (*read)(void*, int sz, int n, void *buf);
 } io·Reader;
 
+typedef struct io·LineReader
+{
+    int (*readln)(void*, int n, void *buf);
+} io·LineReader;
+
 typedef struct io·Peeker
 {
     byte  (*get)(void*);
@@ -175,6 +184,18 @@ typedef struct io·ReadWriter
 } io·ReadWriter;
 
 // -----------------------------------------------------------------------------
+// memory mapped files
+
+typedef struct mmap·Reader 
+{
+    vlong len;
+    void* buf;
+} mmap·Reader;
+
+mmap·Reader mmap·open(byte *name);
+error       mmap·close(mmap·Reader rdr);
+
+// -----------------------------------------------------------------------------
 // libflate
 // NOTE: Experimental!