From f5e6c210a95a98a4381e6142ad599e1ec3f8eff6 Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Wed, 15 May 2013 11:38:31 -0400
Subject: add some error checking

---
 src/c/quikr.c       | 18 +++++++++++++++++-
 src/c/quikr_train.c | 13 +++++++++----
 2 files changed, 26 insertions(+), 5 deletions(-)

diff --git a/src/c/quikr.c b/src/c/quikr.c
index bb21093..e0ba77e 100644
--- a/src/c/quikr.c
+++ b/src/c/quikr.c
@@ -112,7 +112,6 @@ int main(int argc, char **argv) {
     exit(EXIT_FAILURE);
   }
 
-
   if(verbose) { 
     printf("kmer: %d\n", kmer);
     printf("lambda: %d\n", lambda);
@@ -121,11 +120,28 @@ int main(int argc, char **argv) {
     printf("sensing database fasta: %s\n", sensing_fasta_filename);
     printf("output: %s\n", output_filename);
   }
+
+  if(access (sensing_matrix_filename, F_OK) == -1) {
+    fprintf(stderr, "Error: could not find %s\n", sensing_matrix_filename);
+    exit(EXIT_FAILURE);
+  }
+  if(access (sensing_fasta_filename, F_OK) == -1) {
+    fprintf(stderr, "Error: could not find %s\n", sensing_fasta_filename);
+    exit(EXIT_FAILURE);
+  }
+  if(access (input_fasta_filename, F_OK) == -1) {
+    fprintf(stderr, "Error: could not find %s\n", input_fasta_filename);
+    exit(EXIT_FAILURE);
+  }
+
   // 4 "ACGT" ^ Kmer gives us the size of output rows
   width = pow(4, kmer);
   width = width + 1;
 
   sequences = count_sequences(sensing_fasta_filename);
+  if(sequences == 0) {
+    fprintf(stderr, "Error: %s contains 0 fasta sequences\n", sensing_fasta_filename);
+  }
 
   if(verbose) {
     printf("width: %d\nsequences %d\n", width, sequences);
diff --git a/src/c/quikr_train.c b/src/c/quikr_train.c
index f19a554..1585629 100644
--- a/src/c/quikr_train.c
+++ b/src/c/quikr_train.c
@@ -22,7 +22,7 @@ int main(int argc, char **argv) {
 
 
   int c;
-  int kmer = 0;
+  int kmer = 6;
 
   char *fasta_file = NULL;
   char *output_file = NULL;
@@ -88,15 +88,17 @@ int main(int argc, char **argv) {
     exit(EXIT_FAILURE);
   }
 
-  if(kmer == 0)
-    kmer = 6;
-
   if(verbose) {
     printf("kmer size: %d\n", kmer);
     printf("fasta file: %s\n", fasta_file);
     printf("output file: %s\n", output_file);
   }
 
+  if(access (fasta_file, F_OK) == -1) {
+    fprintf(stderr, "Error: could not find %s\n", fasta_file);
+    exit(EXIT_FAILURE);
+  }
+
   if(strcmp(&output_file[strlen(output_file) - 3], ".gz") != 0) {
     char *temp = malloc(sizeof(strlen(output_file) + 4));
     sprintf(temp, "%s.gz", output_file);
@@ -107,6 +109,9 @@ int main(int argc, char **argv) {
   // 4 ^ Kmer gives us the width, or the number of permutations of ACTG with kmer length
   int width = pow(4, kmer);
   int sequences = count_sequences(fasta_file);
+  if(sequences == 0) {
+    fprintf(stderr, "Error: %s contains 0 fasta sequences\n", fasta_file);
+  }
 
   if(verbose)
     printf("sequences: %d\nwidth: %d\n", sequences, width);
-- 
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