Merge pull request #41 from jenniferliddle/devel

Added unit test for array.c, and tidied tests generally

Makefile.am

@@ -1,5 +1,13 @@
 ACLOCAL_AMFLAGS= -I m4
-TESTS = test/t_bamit test/t_chrsplit test/t_select test/t_bclfile test/t_decode test/t_filterfile test/t_posfile test/t_i2b
+TESTS = test/t_array \
+        test/t_bamit \
+        test/t_chrsplit \
+        test/t_select \
+        test/t_bclfile \
+        test/t_decode \
+        test/t_filterfile \
+        test/t_posfile \
+        test/t_i2b
 SUBDIRS = src test
 dist_doc_DATA = README.md LICENSE
 AM_COLOR_TESTS=always

configure.ac

@@ -1,6 +1,5 @@
 AC_INIT([bambi], m4_esyscmd_s([git describe --dirty --always --tags]), [[email protected]])
 AC_ARG_VAR(HTSDIR,Directory to look for hts)
-#AM_INIT_AUTOMAKE([-Wall -Werror foreign subdir-objects tar-pax no-dependencies])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign tar-pax no-dependencies])
 AC_PROG_CC
 

test/Makefile.am

@@ -1,7 +1,7 @@
 AM_CPPFLAGS = $(HTSLIB_CPPFLAGS) -std=gnu99
 AM_LDFLAGS = $(HTSLIB_LDFLAGS)
 
-check_PROGRAMS = t_bamit t_chrsplit t_select t_bclfile t_decode t_filterfile t_posfile t_i2b
+check_PROGRAMS = t_array t_bamit t_chrsplit t_select t_bclfile t_decode t_filterfile t_posfile t_i2b
 
 t_select_SOURCES = t_select.c $(top_srcdir)/src/select.c ../src/array.c ../src/bamit.c ../src/parse.c ../src/hts_addendum.c
 t_select_CFLAGS = -I$(top_srcdir)/src -DDATA_DIR=$(abs_srcdir)/data
@@ -15,6 +15,10 @@ t_bamit_SOURCES = t_bamit.c $(top_srcdir)/src/bamit.c
 t_bamit_CFLAGS = -I$(top_srcdir)/src -DDATA_DIR=$(abs_srcdir)/data
 t_bamit_LDADD = $(HTSLIB_HOME)/lib/libhts.a -lz -ldl -lxml2 -lpthread -llzma -lbz2
 
+t_array_SOURCES = t_array.c $(top_srcdir)/src/array.c 
+t_array_CFLAGS = -I$(top_srcdir)/src -DDATA_DIR=$(abs_srcdir)/data
+t_array_LDADD = $(HTSLIB_HOME)/lib/libhts.a -lz -ldl -lxml2 -lpthread -llzma -lbz2
+
 t_bclfile_SOURCES = t_bclfile.c
 t_bclfile_CFLAGS = -DDATA_DIR=$(abs_srcdir)/data
 t_bclfile_LDADD = -lz -ldl -lxml2 -lpthread

test/data/select_1_human.sam

@@ -108,4 +108,4 @@ IL16_986:1:9:9:307	129	12	54468914	0	37M	1	90707227	0	AAAAAAAAAAAAAAAAAAAAAAAAAA
 IL16_986:1:9:9:47	113	5	34606831	0	37M	1	187335121	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	X0:i:24815	MD:Z:37	RG:Z:1	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
 IL16_986:1:9:9:47	177	1	187335121	0	37M	5	34606831	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	X0:i:24815	MD:Z:37	RG:Z:1	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
 IL16_986:1:9:9:954	113	6	84008653	0	37M	5	143379477	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>	X0:i:24815	MD:Z:37	RG:Z:1	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
-IL16_986:1:9:9:954	177	5	143379477	0	37M	6	84008653	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	X0:i:24815	MD:Z:37	RG:Z:1	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R
+IL16_986:1:9:9:954	173	5	143379477	0	37M	6	84008653	0	TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT	<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<	X0:i:24815	MD:Z:37	RG:Z:1	XG:i:0	AM:i:0	NM:i:0	SM:i:0	XM:i:0	XO:i:0	XT:A:R

test/t_array.c

@@ -0,0 +1,96 @@
+/*  t_array.c -- array test cases.
+
+    Copyright (C) 2016 Genome Research Ltd.
+
+    Author: Jennifer Liddle <[email protected]>
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU Affero General Public License as published
+by the Free Software Foundation, either version 3 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU Affero General Public License for more details.
+
+You should have received a copy of the GNU Affero General Public License
+along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+*/
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <unistd.h>
+#include <string.h>
+#include "array.h"
+#include "htslib/hts.h"
+
+#define xMKNAME(d,f) #d f
+#define MKNAME(d,f) xMKNAME(d,f)
+
+
+int verbose = 0;
+
+int success = 0;
+int failure = 0;
+
+void checkEqual(char *name, char *expected, char *actual)
+{
+    if (actual == NULL) actual = "<null>";
+    if (strcmp(expected, actual)) {
+        fprintf(stderr, "%s: Expected: %s \tGot: %s\n", name, expected, actual);
+        failure++;
+    }
+}
+
+void icheckEqual(char *name, int expected, int actual)
+{
+    if (expected != actual) {
+        fprintf(stderr, "%s: Expected: %d \tGot: %d\n", name, expected, actual);
+        failure++;
+    }
+}
+
+int main(int argc, char**argv)
+{
+    va_t *va = va_init(2,free);
+    ia_t *ia = ia_init(3);
+
+    icheckEqual("va Initially empty", true, va_isEmpty(va));
+    icheckEqual("ia Initially empty", true, ia_isEmpty(ia));
+
+    va_push(va,strdup("Hello world"));
+    ia_push(ia, 1);
+    icheckEqual("va one item", 1, va->end);    
+    icheckEqual("ia one item", 1, ia->end);    
+
+    va_push(va,strdup("xyzzy"));
+    ia_push(ia, 2);
+    va_push(va,strdup("xyzzy"));
+    ia_push(ia, 3);
+    va_push(va,strdup("xyzzy"));
+    ia_push(ia, 9);
+    va_push(va,strdup("plugh"));
+    ia_push(ia, 5);
+    icheckEqual("va five items", 5, va->end);    
+    icheckEqual("ia five items", 5, ia->end);    
+
+    checkEqual("va first item", "Hello world", va->entries[0]);
+    icheckEqual("ia first item", 1, ia->entries[0]);
+    checkEqual("va last item", "plugh", va->entries[va->end-1]);
+    icheckEqual("ia last item", 5, ia->entries[ia->end-1]);
+
+    ia_sort(ia);
+    icheckEqual("ia sort first", 1, ia->entries[0]);
+    icheckEqual("ia sort last", 9, ia->entries[ia->end-1]);
+
+    char *s = ia_join(ia,"xyz");
+    checkEqual("ia join", "1xyz2xyz3xyz5xyz9", s);
+
+    ia_free(ia);
+    va_free(va);
+
+    printf("array tests: %s\n", failure ? "FAILED" : "Passed");
+    return failure ? EXIT_FAILURE : EXIT_SUCCESS;
+}

test/t_bamit.c

@@ -106,4 +106,7 @@ int main(int argc, char**argv)
     icheckEqual("Number of records", 6, n);
     icheckEqual("End of records", false, BAMit_hasnext(bit));
     BAMit_free(bit);
+
+    printf("BAMit tests: %s\n", failure ? "FAILED" : "Passed");
+    return failure ? EXIT_FAILURE : EXIT_SUCCESS;
 }

test/t_chrsplit.c

@@ -264,6 +264,6 @@ int main(int argc, char**argv)
     testxahuman(TMPDIR);
     testxahuman_exclude_unaligned(TMPDIR);
 
-    printf("select tests: %s\n", failure ? "FAILED" : "Passed");
+    printf("chrsplit tests: %s\n", failure ? "FAILED" : "Passed");
     return failure ? EXIT_FAILURE : EXIT_SUCCESS;
 }