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Minor patches for easier porting and packaging #895

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Minor patches for easier porting and packaging #895

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e2c713f
Minor patches for easier porting
Jan 24, 2021
9f5c8c9
Simple patch to silence most compiler warnings
Jan 24, 2021
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13 changes: 8 additions & 5 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,8 @@
# (c) 2009 Aaron Quinlan
# ==========================

SHELL := /bin/bash -e
# Use sh for portability and avoid bash extensions in shell commands
SHELL := /bin/sh -e

VERSION_FILE=./src/utils/version/version_git.h
RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
Expand All @@ -21,7 +22,8 @@ OBJ_DIR = obj
BIN_DIR = bin
SRC_DIR = src

CXX = g++
# Default if not provided via the environment or make args
CXX ?= g++

ifeq ($(DEBUG),1)
BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
Expand All @@ -41,7 +43,8 @@ endif
BT_LDFLAGS =
BT_LIBS = -lz -lm -lbz2 -llzma -lpthread

prefix ?= /usr/local
# Default if not provided via the environment or make args
PREFIX ?= /usr/local

SUBDIRS = $(SRC_DIR)/annotateBed \
$(SRC_DIR)/bamToBed \
Expand Down Expand Up @@ -197,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
.PHONY: all

install: all
mkdir -p $(DESTDIR)$(prefix)/bin
mkdir -p $(DESTDIR)$(PREFIX)/bin
for file in bin/* ; do \
cp -f $$file $(DESTDIR)$(prefix)/bin; \
cp -f $$file $(DESTDIR)$(PREFIX)/bin; \
done

print_banner:
Expand Down
7 changes: 6 additions & 1 deletion src/utils/BamTools/include/SamHeader.hpp
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Expand Up @@ -7,6 +7,7 @@
#include <string.h>
#include <api/BamAux.h>
#include <stdlib.h>
#include <sysexits.h>


#ifdef WITH_HTS_CB_API
Expand All @@ -29,7 +30,11 @@ namespace htslib_future {
ops.cb_data = buffer;
samFile* fp = hts_open_callback(NULL, &ops, "w");

sam_hdr_write(fp, hdr);
if ( sam_hdr_write(fp, hdr) != 0 )
{
fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
exit(EX_IOERR);
}

hts_close(fp);

Expand Down
15 changes: 9 additions & 6 deletions src/utils/htslib/Makefile
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Expand Up @@ -22,20 +22,23 @@
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.

CC = gcc
AR = ar
RANLIB = ranlib
# Defaults if not provided by the environment or make args
CC ?= gcc
AR ?= ar
RANLIB ?= ranlib

# Default libraries to link if configure is not used
htslib_default_libs = -lz -lm -lbz2 -llzma

CPPFLAGS =
# Defaults if not provided by the environment or make args
CPPFLAGS ?=
CFLAGS ?= -g -Wall -O2
LDFLAGS ?=

# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
# For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
CFLAGS = -g -Wall -O2
EXTRA_CFLAGS_PIC = -fpic
LDFLAGS =
LIBS = $(htslib_default_libs)

prefix = /usr/local
Expand Down