Much simpler faster code for parsing fastq files.

[fastq-tools.git] / src / fastq-uniq.c

diff --git a/src/fastq-uniq.c b/src/fastq-uniq.c
index 32d344e29e1abfd10fa44203b1d94c1861fd8974..3a92565c8a5118dbd2b13fd4720347058f619709 100644 (file)
--- a/src/fastq-uniq.c
+++ b/src/fastq-uniq.c
@@ -13,6 +13,7 @@
 #include "hash.h"
 #include "parse.h"
 #include <string.h>
+#include <inttypes.h>
 #include <zlib.h>
 #include <getopt.h>
 
@@ -48,10 +49,10 @@ static size_t total_reads;
 
 void fastq_hash(FILE* fin, hash_table* T)
 {
-    fastq_t* fqf = fastq_open(fin);
-    seq_t* seq = fastq_alloc_seq();
+    fastq_t* fqf = fastq_create(fin);
+    seq_t* seq = seq_create();
 
-    while (fastq_next(fqf, seq)) {
+    while (fastq_read(fqf, seq)) {
         inc_hash_table(T, seq->seq.s, seq->seq.n);
 
         total_reads++;
@@ -60,8 +61,8 @@ void fastq_hash(FILE* fin, hash_table* T)
         }
     }
 
-    fastq_free_seq(seq);
-    fastq_close(fqf);
+    seq_free(seq);
+    fastq_free(fqf);
 }
 
 
@@ -84,7 +85,7 @@ void print_hash_table(FILE* fout, hash_table* T)
 
     size_t i;
     for (i = 0; i < T->m; i++) {
-        fprintf(fout, ">unique-read-%07zu (%zu copies)\n", i, S[i]->count);
+        fprintf(fout, ">unique-read-%07zu (%"PRIu32" copies)\n", i, S[i]->count);
         fwrite(S[i]->value, S[i]->len, sizeof(char), fout);
         fprintf(fout, "\n");
     }