feat: parsing multiline fastq files

1 files changed, 59 insertions, 0 deletions

diff --git a/sys/libbio/test.c b/sys/libbio/test.c
index f301ead..e943153 100644
--- a/sys/libbio/test.c
+++ b/sys/libbio/test.c
@@ -3,6 +3,16 @@
 #include <libbio.h>
 
 #include <time.h>
+#include "kseq.h"
+
+static
+int
+my_read(Stream *s, void *buf, int n)
+{
+    return io·read(s, 1, n, buf);
+}
+
+KSEQ_INIT(Stream*, my_read)
 
 // -----------------------------------------------------------------------
 // Point of entry for testing
@@ -31,6 +41,7 @@ test·newick()
     err = bio·writenewick(t, wtr, fd[1]);
 
     io·flush(fd[1]);
+
     io·close(fd[0]); 
     io·close(fd[1]);
 
@@ -86,6 +97,50 @@ test·fasta()
 }
 
 error
+test·fastq()
+{
+    error err;
+    Stream           *fd;
+
+    bio·Seq          seq;
+    bio·FastqReader *rdr;
+
+    clock_t t;
+
+    int  n, slen;
+    kseq_t *kseq;
+
+    fd  = io·open("/home/nolln/root/data/test/eg.fq", "r");
+
+    t    = clock();
+	kseq = kseq_init(fd);
+	while (kseq_read(kseq) >= 0) {
+		++n, slen += kseq->seq.l;
+    }
+    t = clock() - t;
+    printf("heng's fastq code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
+
+	kseq_destroy(kseq);
+
+    io·seek(fd, 0, seek·set);
+
+    rdr = bio·openfastq((io·Reader){.read = &io·read}, fd, mem·sys, nil);
+
+    t = clock();
+    err = 0;
+    while (!err) {
+        err = bio·readfastq(rdr, &seq);
+    }
+    t = clock() - t;
+    printf("nick's fastq code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
+    bio·closefastq(rdr);
+
+
+    io·close(fd); 
+    return err <= 0 ? 0 : 1;
+}
+
+error
 main()
 {
     error err;
@@ -96,5 +151,9 @@ main()
     if (err = test·fasta(), err) {
         errorf("test fail: fasta");
     }
+
+    if (err = test·fastq(), err) {
+        errorf("test fail: fastq");
+    }
 }