From 42c2a6b10b6313b7f87189f1467996fc3cf18e24 Mon Sep 17 00:00:00 2001
From: Daniel Jones <dcjones@cs.washington.edu>
Date: Sat, 8 Dec 2012 19:41:17 -0800
Subject: [PATCH] Rename hash to hash_table.

---
 TODO                         | 39 +++++++-----------------------------
 configure.ac                 |  4 ++--
 src/Makefile.am              |  4 ++--
 src/fastq-sort.c             |  4 ++--
 src/fastq-uniq.c             |  2 +-
 src/{hash.c => hash_table.c} |  2 +-
 src/{hash.h => hash_table.h} |  0
 7 files changed, 15 insertions(+), 40 deletions(-)
 rename src/{hash.c => hash_table.c} (99%)
 rename src/{hash.h => hash_table.h} (100%)

diff --git a/TODO b/TODO
index 4afc59a..7b06a07 100644
--- a/TODO
+++ b/TODO
@@ -1,35 +1,16 @@
 
-general
-=======
+Rename hash.h/c to hash_table.h/c.
 
-Man pages!
+Seperate murmurhash into it's own file: hash.h/hash.c.
 
+Document fastq-sort.
 
-I would like to encorporate some domain-specific compression algorithm. Options
-I know of:
-  * G-SQZ (http://www.tgen.org/research/gsqueez.cfm) : not open source (i.e. not an option)
-  * fqzcomp (http://seqanswers.com/forums/archive/index.php/t-6349.html)
-  * DSRC (http://bioinformatics.oxfordjournals.org/cgi/content/short/27/6/860?rss=1) :
-    Not yet available?
-  * Invent my own.
+More comparison functions for fastq-sort.
 
+Link against quip so we can run these tools on quip/fastq/bam/sam with one
+interface.
 
-
-
-
-
-program specific
-================
-
-
-fastq-grep
-----------
-
-
-
-fastq-kmers
------------
-
+Make a website for fastq-tools.
 
 
 fastq-match
@@ -43,9 +24,3 @@ might look to Phil Green's cross_match implementation for ideas.
 An option to return the sequences that match past a certain threshold would be
 useful.
 
-
-
-fastq-uniq
-----------
-
-
diff --git a/configure.ac b/configure.ac
index 93e89b0..f1e45d9 100644
--- a/configure.ac
+++ b/configure.ac
@@ -16,8 +16,8 @@ m4_ifdef([AC_TYPE_UINT64_T], [AC_TYPE_UINT64_T])
 m4_ifdef([AC_TYPE_SIZE_T],   [AC_TYPE_SIZE_T])
 m4_ifdef([AC_HEADER_STDBOOL], [AC_HEADER_STDBOOL])
 
-opt_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O3"
-dbg_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O0"
+opt_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O3 -D_C99_SOURCE"
+dbg_CFLAGS="--std=c99 -Wall -Wextra -pedantic -g -O0 -D_C99_SOURCE"
 
 AC_ARG_ENABLE([debug],
               [AS_HELP_STRING([--enable-debug],
diff --git a/src/Makefile.am b/src/Makefile.am
index 1fc7d3a..e3cbee3 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -4,7 +4,7 @@ bin_PROGRAMS = fastq-grep fastq-kmers fastq-match fastq-uniq fastq-qual fastq-sa
 fastq_common_src=common.h common.c
 fastq_parse_src=parse.h parse.c
 fastq_sw_src=sw.h sw.c
-fastq_hash_src=hash.h hash.c
+fastq_hash_table_src=hash_table.h hash_table.c
 fastq_rng_src=rng.h rng.c
 
 fastq_grep_SOURCES = fastq-grep.c $(fastq_common_src) $(fastq_parse_src)
@@ -14,7 +14,7 @@ fastq_kmers_SOURCES = fastq-kmers.c $(fastq_common_src) $(fastq_parse_src)
 
 fastq_match_SOURCES = fastq-match.c $(fastq_common_src) $(fastq_parse_src) $(fastq_sw_src)
 
-fastq_uniq_SOURCES = fastq-uniq.c $(fastq_common_src) $(fastq_parse_src) $(fastq_hash_src)
+fastq_uniq_SOURCES = fastq-uniq.c $(fastq_common_src) $(fastq_parse_src) $(fastq_hash_table_src)
 
 fastq_qual_SOURCES = fastq-qual.c $(fastq_common_src) $(fastq_parse_src)
 
diff --git a/src/fastq-sort.c b/src/fastq-sort.c
index ff77441..2876b9f 100644
--- a/src/fastq-sort.c
+++ b/src/fastq-sort.c
@@ -3,8 +3,8 @@
  *
  * 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.
  *
  */
 
diff --git a/src/fastq-uniq.c b/src/fastq-uniq.c
index 3a92565..f77a10c 100644
--- a/src/fastq-uniq.c
+++ b/src/fastq-uniq.c
@@ -10,7 +10,7 @@
 
 
 #include "common.h"
-#include "hash.h"
+#include "hash_table.h"
 #include "parse.h"
 #include <string.h>
 #include <inttypes.h>
diff --git a/src/hash.c b/src/hash_table.c
similarity index 99%
rename from src/hash.c
rename to src/hash_table.c
index 25202a4..c8878a0 100644
--- a/src/hash.c
+++ b/src/hash_table.c
@@ -7,7 +7,7 @@
  */
 
 
-#include "hash.h"
+#include "hash_table.h"
 #include "common.h"
 #include <stdlib.h>
 #include <stdint.h>
diff --git a/src/hash.h b/src/hash_table.h
similarity index 100%
rename from src/hash.h
rename to src/hash_table.h
-- 
2.39.2