Ensure that sample IDs don't contain weird chars

This ensures that the file names created don't contain them either.

CMakeLists.txt

@@ -26,7 +26,6 @@ MESSAGE(STATUS "${CMAKE_BUILD_TYPE} build of axe version: ${AXE_VERSION}")
 
 INCLUDE(CheckSymbolExists)
 INCLUDE(CheckIncludeFiles)
-CHECK_INCLUDE_FILES(regex.h REGEX_H_FOUND)
 FIND_PACKAGE(ZLIB 1.2.5 REQUIRED)
 FIND_PACKAGE(GSL 1.5 REQUIRED)
 SET(AXE_DEPENDS_LIBS

TODO.md

@@ -1,8 +1,6 @@
 TODO list:
 ==========
 
-- Check that a sample's name doesn't contain weird characters that shouldn't be
-  in file names. (i.e.: '"\[]{}()/!@#$%^&*;: )
 - Re-read documentation; fix errors
 - Exhaustive CLI tests
 - Refactor trie lookups to hide all datrie operations from main body of code

src/axe.c

@@ -243,7 +243,9 @@ axe_read_barcodes(struct axe_config *config)
     struct axe_barcode **barcodes = NULL;
     size_t n_barcode_pairs = 0; /* Entries in file */
     size_t n_barcodes_alloced = 8;
+    const char *bad_fname_chars = "'\"!@#$%^&*()+=~`[]{}\\|;:/?><,";
     char *line = NULL;
+    char *tmp = NULL;
     size_t linesz = 128;
     ssize_t linelen = 0;
     size_t iii = 0;
@@ -281,6 +283,12 @@ axe_read_barcodes(struct axe_config *config)
             fprintf(stderr, "Couldn't parse barcode line '%s'\n", line);
             goto error;
         }
+        /* Replace all bad chars with '-' */
+        tmp = strpbrk(this_barcode->id, bad_fname_chars);
+        while (tmp != NULL) {
+            *tmp = '-'; /* Replace with dash */
+            tmp = strpbrk(tmp + 1, bad_fname_chars);
+        }
         /* Add the barcode to the array */
         barcodes[n_barcode_pairs++] = this_barcode;
     }