From 622ec3cadbda926e02af594d2ff7e89d33833b36 Mon Sep 17 00:00:00 2001
From: Nicholas Noll <nbnoll@eml.cc>
Date: Sat, 25 Apr 2020 12:43:11 -0700
Subject: chore: prepare for refactoring to allow for fastq

---
 sys/libbio/io/fasta.c | 28 +++++++++++++++++++++++++---
 sys/libbio/test.c     | 35 +++++++++++++++++++++++++++++++----
 2 files changed, 56 insertions(+), 7 deletions(-)

(limited to 'sys')

diff --git a/sys/libbio/io/fasta.c b/sys/libbio/io/fasta.c
index 891e222..5e659ab 100644
--- a/sys/libbio/io/fasta.c
+++ b/sys/libbio/io/fasta.c
@@ -132,15 +132,18 @@ fill(bio·FastaReader *rdr)
     return 0;
 }
 
+// -----------------------------------------------------------------------
+// Fasta files
+
 bio·FastaReader*
-bio·newfastareader(io·Reader stream, void *s, mem·Allocator heap, void *h)
+bio·openfasta(io·Reader file, void *f, mem·Allocator heap, void *h)
 {
     error err;
     bio·FastaReader *rdr;
 
     rdr = heap.alloc(h, 1, sizeof(bio·FastaReader));
-    rdr->file = stream;
-    rdr->f    = s;
+    rdr->file = file;
+    rdr->f    = f;
     rdr->eof  = 0;
 
     rdr->seq = heap.alloc(h, 1, sizeof(*rdr->seq) + INIT_NM_SIZE + INIT_SQ_SIZE);
@@ -236,3 +239,22 @@ SUCCESS:
 
     return 0;
 }
+
+error
+bio·closefasta(bio·FastaReader *rdr)
+{
+    mem·Allocator heap;
+    void         *h;
+
+
+    heap = rdr->seq->heap;
+    h    = rdr->seq->h; 
+    
+    heap.free(h, rdr->seq);
+    heap.free(h, rdr);
+
+    return 0;
+}
+
+// -----------------------------------------------------------------------
+// Fastq files
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index 14f2b06..d38bbc1 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -2,6 +2,9 @@
 #include <libn.h>
 #include <libbio.h>
 
+#include <time.h>
+#include "kseq.h"
+
 // -----------------------------------------------------------------------
 // Point of entry for testing
 
@@ -32,6 +35,7 @@ test·newick()
     io·close(fd[0]); 
     io·close(fd[1]);
 
+    mem·freearena(mem);
     return 0;
 }
 
@@ -44,16 +48,39 @@ test·fasta()
     bio·Seq          seq;
     bio·FastaReader *rdr;
 
+    clock_t t;
+
     fd  = io·open("/home/nolln/root/data/test/zika.fa", "r");
-    rdr = bio·newfastareader((io·Reader){.read = &io·read}, fd, mem·sys, nil);
 
+    /* Benchmark against Heng */
+#if 0
+    int  n, slen;
+    kseq_t *kseq;
+
+    t    = clock();
+	kseq = kseq_init(fd);
+	while (kseq_read(kseq) >= 0) {
+		++n, slen += kseq->seq.l;
+    }
+    t = clock() - t;
+    printf("heng's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
+
+	kseq_destroy(kseq);
+
+    io·seek(fd, 0, seek·set);
+#endif
+
+    rdr = bio·openfasta((io·Reader){.read = &io·read}, fd, mem·sys, nil);
+
+    t = clock();
     err = 0;
     while (!err) {
         err = bio·readfasta(rdr, &seq);
-        if (!err) {
-            printf(">%s\n", seq.name);
-        }
     }
+    t = clock() - t;
+    printf("nick's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
+    bio·closefasta(rdr);
+
 
     io·close(fd); 
     return err <= 0 ? 0 : 1;
-- 
cgit v1.2.1