X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ffastq-sort.c;h=9799b075348ad087ef6df654f075618db0af4e50;hb=52779892ccc2ac676654a34baff8d1e7645121de;hp=e96d9bf5164c9711aa965e05a4a47868929e7ffd;hpb=1860da1d6d887e658671c60a1ec47cb3cb80449e;p=fastq-tools.git

diff --git a/src/fastq-sort.c b/src/fastq-sort.c
index e96d9bf..9799b07 100644
--- a/src/fastq-sort.c
+++ b/src/fastq-sort.c
@@ -3,12 +3,13 @@
  *
  * Copyright (c) 2012 by Daniel C. Jones <dcjones@cs.washington.edu>
  *
- * fastq-sample :
- * Sample reads with or without replacement from a FASTQ file.
+ * fastq-sort:
+ * Sort fastq files efficiently.
  *
  */
 
 #include <assert.h>
+#include <ctype.h>
 #include <getopt.h>
 #include <string.h>
 #include <unistd.h>
@@ -245,22 +246,22 @@ bool seq_array_push(seq_array_t* a, const seq_t* seq)
 
     memcpy(&a->data[a->data_used], seq->id1.s, seq->id1.n + 1);
     a->seqs[a->n].id1.s = &a->data[a->data_used];
-    a->seqs[a->n].id1.n = seq->id1.n + 1;
+    a->seqs[a->n].id1.n = seq->id1.n;
     a->data_used += seq->id1.n + 1;
 
     memcpy(&a->data[a->data_used], seq->seq.s, seq->seq.n + 1);
     a->seqs[a->n].seq.s = &a->data[a->data_used];
-    a->seqs[a->n].seq.n = seq->seq.n + 1;
+    a->seqs[a->n].seq.n = seq->seq.n;
     a->data_used += seq->seq.n + 1;
 
     memcpy(&a->data[a->data_used], seq->id2.s, seq->id2.n + 1);
     a->seqs[a->n].id2.s = &a->data[a->data_used];
-    a->seqs[a->n].id2.n = seq->id2.n + 1;
+    a->seqs[a->n].id2.n = seq->id2.n;
     a->data_used += seq->id2.n + 1;
 
     memcpy(&a->data[a->data_used], seq->qual.s, seq->qual.n + 1);
     a->seqs[a->n].qual.s = &a->data[a->data_used];
-    a->seqs[a->n].qual.n = seq->qual.n + 1;
+    a->seqs[a->n].qual.n = seq->qual.n;
     a->data_used += seq->qual.n + 1;
 
     ++a->n;
@@ -357,6 +358,20 @@ void print_help()
 }
 
 
+/* Parse a size specification, which is just a number with a K, M, G suffix. */
+size_t parse_size(const char* str)
+{
+    char* endptr;
+    unsigned long size = strtoul(str, &endptr, 10);
+
+    if      (toupper(*endptr) == 'K') size *= 1000;
+    else if (toupper(*endptr) == 'M') size *= 1000000;
+    else if (toupper(*endptr) == 'G') size *= 1000000000;
+
+    return size;
+}
+
+
 int main(int argc, char* argv[])
 {
     int opt, opt_idx;
@@ -366,29 +381,34 @@ int main(int argc, char* argv[])
 
     static struct option long_options[] =
     {
-        {"reverse", no_argument, NULL, 'r'},
-        {"id",      no_argument, NULL, 'I'},
-        {"seq",     no_argument, NULL, 'S'},
-        {"random",  no_argument, NULL, 'R'},
-        {"help",    no_argument, NULL, 'h'},
-        {"version", no_argument, NULL, 'V'},
+        {"buffer-size", required_argument, NULL, 'S'},
+        {"reverse",     no_argument, NULL, 'r'},
+        {"id",          no_argument, NULL, 'i'},
+        {"seq",         no_argument, NULL, 's'},
+        {"random",      no_argument, NULL, 'R'},
+        {"help",        no_argument, NULL, 'h'},
+        {"version",     no_argument, NULL, 'V'},
         {0, 0, 0, 0}
     };
 
     while (true) {
-        opt = getopt_long(argc, argv, "rISRhV", long_options, &opt_idx);
+        opt = getopt_long(argc, argv, "S:risRhV", long_options, &opt_idx);
         if (opt == -1) break;
 
         switch (opt) {
+            case 'S':
+                buffer_size = parse_size(optarg);
+                break;
+
             case 'r':
                 reverse_sort = true;
                 break;
 
-            case 'I':
+            case 'i':
                 user_cmp = seq_cmp_id;
                 break;
 
-            case 'S':
+            case 's':
                 user_cmp = seq_cmp_seq;
                 break;