From 5fd056c15a0ea0eb28d0bc7cac84d6fa7fe0a3f3 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 30 Sep 2016 13:23:10 +1000
Subject: add fasta parser

---
 dict.c | 67 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------
 1 file changed, 58 insertions(+), 9 deletions(-)

diff --git a/dict.c b/dict.c
index 7bb0e63..53e18bd 100644
--- a/dict.c
+++ b/dict.c
@@ -50,8 +50,9 @@ new_tokeniser(char *path)
   return tok;
 }
 
+// Fastq tokeniser
 int
-getTok(tokeniser *tok)
+getTokQ(tokeniser *tok)
 {
   int c;
   switch(tok->s){
@@ -86,10 +87,48 @@ getTok(tokeniser *tok)
   }
 }
 
+// Fasta tokeniser
+int
+getTokA(tokeniser *tok)
+{
+  int c;
+  switch(tok->s){
+    case TOUTSEQ:
+      c = gzgetc(tok->f);
+      while(c != -1 && c != '>') c = gzgetc(tok->f);
+      while(c != -1 && c != '\n') c = gzgetc(tok->f);
+      tok->s = TINSEQ;
+    case TINSEQ:
+      c = gzgetc(tok->f);
+      while(c != -1 && c == '\n') c = gzgetc(tok->f);
+      switch(c){
+        case -1:
+          return -1;
+        case 'A':
+        case 'a':
+          return 0;
+        case 'C':
+        case 'c':
+          return 1;
+        case 'G':
+        case 'g':
+          return 2;
+        case 'T':
+        case 't':
+          return 3;
+        case '>':
+          while(c != -1 && c != '\n') c = gzgetc(tok->f);
+        default:
+          return -2;
+      }
+  }
+}
+
 void
-usage(char *name)
+usage(void)
 {
-  fprintf(stderr, "usage: %s <input fastq> <bloom output>\n", name);
+  fprintf(stderr, "usage: %s [-a] <input fastq/fasta> <bloom output>\n", argv0);
+  fprintf(stderr, "\t-a: assume input is fasta, default is fastq\n");
   exit(-1);
 }
 
@@ -107,15 +146,25 @@ uint64_t bitmix(uint64_t x)
 int
 main(int argc, char **argv)
 {
-  if(argc != 3)
-    usage(argv[0]);
+  int (*getTok)(tokeniser *) = getTokQ;
+  ARGBEGIN{
+    case 'a':
+      getTok = getTokA;
+      break;
+    case 'h':
+    default:
+      usage();
+  }ARGEND;
+
+  if(argc != 2)
+    usage();
 
-  tokeniser *t = new_tokeniser(argv[1]);
+  tokeniser *t = new_tokeniser(argv[0]);
 
   // map bloom filter
   uint64_t *bloom;
-  if(access(argv[2], F_OK) == -1){
-    int bfd = open(argv[2], O_RDWR | O_CREAT, S_IRUSR | S_IWUSR);
+  if(access(argv[1], F_OK) == -1){
+    int bfd = open(argv[1], O_RDWR | O_CREAT, S_IRUSR | S_IWUSR);
     if(bfd == -1)
       error("open");
     if(ftruncate(bfd, BLOOMSIZE * sizeof(uint64_t)) == -1)
@@ -126,7 +175,7 @@ main(int argc, char **argv)
     bzero(bloom, BLOOMSIZE * sizeof(uint64_t));
   }else{
     struct stat sb;
-    int bfd = open(argv[2], O_RDWR);
+    int bfd = open(argv[1], O_RDWR);
     if(bfd == -1)
       error("open");
     if(fstat(bfd, &sb) == -1)
-- 
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