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Add #include <config.h> to all *.c source files [minor]
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Upcoming config.h settings will have ODR implications, so ensure all
source code sees these settings.

Also add missing faidx.o rule.
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@jmarshall
jmarshall committed Jan 28, 2016
1 parent 664cc5f commit 74a3e0a
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Showing 59 changed files with 175 additions and 58 deletions.
117 changes: 59 additions & 58 deletions Makefile
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@@ -1,6 +1,6 @@
# Makefile for samtools, utilities for the Sequence Alignment/Map format.
#
# Copyright (C) 2008-2015 Genome Research Ltd.
# Copyright (C) 2008-2016 Genome Research Ltd.
# Portions copyright (C) 2010-2012 Broad Institute.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
Expand Down Expand Up @@ -147,49 +147,50 @@ sam_h = sam.h $(htslib_sam_h) $(bam_h)
sam_opts_h = sam_opts.h $(htslib_hts_h)
sample_h = sample.h $(htslib_kstring_h)

bam.o: bam.c $(bam_h) $(htslib_kstring_h) sam_header.h
bam2bcf.o: bam2bcf.c $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h)
bam2depth.o: bam2depth.c $(htslib_sam_h) samtools.h $(sam_opts_h)
bam_addrprg.o: bam_addrprg.c $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
bam_aux.o: bam_aux.c $(bam_h)
bam_cat.o: bam_cat.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h)
bam_color.o: bam_color.c $(bam_h)
bam_import.o: bam_import.c $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
bam_index.o: bam_index.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
bam_lpileup.o: bam_lpileup.c $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
bam_mate.o: bam_mate.c $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h)
bam_md.o: bam_md.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h)
bam_plbuf.o: bam_plbuf.c $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
bam_plcmd.o: bam_plcmd.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
bam_quickcheck.o: bam_quickcheck.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h)
bam_reheader.o: bam_reheader.c $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
bam_rmdup.o: bam_rmdup.c $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h)
bam_rmdupse.o: bam_rmdupse.c $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h)
bam_sort.o: bam_sort.c $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h)
bam_split.o: bam_split.c $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h)
bam_stat.o: bam_stat.c $(htslib_sam_h) samtools.h
bam_tview.o: bam_tview.c $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h)
bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h
bam2bcf.o: bam2bcf.c config.h $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) errmod.h
bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_sam_h) $(bam2bcf_h) kprobaln.h $(htslib_khash_h) $(htslib_ksort_h)
bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)
bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
bam_aux.o: bam_aux.c config.h $(bam_h)
bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h)
bam_color.o: bam_color.c config.h $(bam_h)
bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h)
bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) kprobaln.h $(sam_opts_h)
bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_bgzf_h)
bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) $(bam_h) $(htslib_khash_h)
bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h)
bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h)
bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(sam_opts_h)
bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h
bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) $(sam_opts_h)
bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
bam_tview_html.o: bam_tview_html.c $(bam_tview_h)
bam_flags.o: bam_flags.c $(htslib_sam_h)
bamshuf.o: bamshuf.c $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
bamtk.o: bamtk.c $(htslib_hts_h) samtools.h version.h
bedcov.o: bedcov.c $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
bedidx.o: bedidx.c $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
cut_target.o: cut_target.c $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h)
dict.o: dict.c $(htslib_kseq_h) $(htslib_hts_h)
errmod.o: errmod.c errmod.h $(htslib_ksort_h)
kprobaln.o: kprobaln.c kprobaln.h
padding.o: padding.c $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h)
phase.o: phase.c $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
sam.o: sam.c $(htslib_faidx_h) $(sam_h)
sam_header.o: sam_header.c sam_header.h $(htslib_khash_h)
sam_opts.o: sam_opts.c $(sam_opts_h)
sam_view.o: sam_view.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
sample.o: sample.c $(sample_h) $(htslib_khash_h)
stats_isize.o: stats_isize.c stats_isize.h $(htslib_khash_h)
stats.o: stats.c $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h)
bam_flags.o: bam_flags.c config.h $(htslib_sam_h)
bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h
bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
cut_target.o: cut_target.c config.h $(htslib_sam_h) errmod.h $(htslib_faidx_h) $(sam_opts_h)
dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)
errmod.o: errmod.c config.h errmod.h $(htslib_ksort_h)
faidx.o: faidx.c config.h $(htslib_faidx_h)
kprobaln.o: kprobaln.c config.h kprobaln.h
padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h)
phase.o: phase.c config.h $(htslib_sam_h) errmod.h $(sam_opts_h) $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)
sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)
sam_opts.o: sam_opts.c config.h $(sam_opts_h)
sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)
stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)


# test programs
Expand Down Expand Up @@ -236,15 +237,15 @@ test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)

test_test_h = test/test.h $(htslib_sam_h)

test/merge/test_bam_translate.o: test/merge/test_bam_translate.c bam_sort.o $(test_test_h)
test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c bam_sort.o
test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c bam_sort.o
test/split/test_count_rg.o: test/split/test_count_rg.c bam_split.o $(test_test_h)
test/split/test_expand_format_string.o: test/split/test_expand_format_string.c bam_split.o $(test_test_h)
test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c bam_split.o $(test_test_h)
test/split/test_parse_args.o: test/split/test_parse_args.c bam_split.o $(test_test_h)
test/test.o: test/test.c $(htslib_sam_h) $(test_test_h)
test/vcf-miniview.o: test/vcf-miniview.c $(htslib_vcf_h)
test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h)
test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o
test/merge/test_trans_tbl_init.o: test/merge/test_trans_tbl_init.c config.h bam_sort.o
test/split/test_count_rg.o: test/split/test_count_rg.c config.h bam_split.o $(test_test_h)
test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)
test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)
test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)
test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)
test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)


# misc programs
Expand All @@ -267,15 +268,15 @@ misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
misc/wgsim: misc/wgsim.o
$(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)

misc/ace2sam.o: misc/ace2sam.c $(htslib_kstring_h) $(htslib_kseq_h)
misc/md5fa.o: misc/md5fa.c $(htslib_kseq_h) $(htslib_hts_h)
misc/md5sum-lite.o: misc/md5sum-lite.c $(htslib_hts_h)
misc/wgsim.o: misc/wgsim.c $(htslib_kseq_h)
misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h)
misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h)
misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h)
misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h)

misc/maq2sam-short.o: misc/maq2sam.c
misc/maq2sam-short.o: misc/maq2sam.c config.h
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c

misc/maq2sam-long.o: misc/maq2sam.c
misc/maq2sam-long.o: misc/maq2sam.c config.h
$(CC) $(CFLAGS) -DMAQ_LONGREADS $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c


Expand Down
2 changes: 2 additions & 0 deletions bam.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdio.h>
#include <ctype.h>
#include <errno.h>
Expand Down
2 changes: 2 additions & 0 deletions bam2bcf.c
View file
Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <math.h>
#include <stdint.h>
#include <assert.h>
Expand Down
2 changes: 2 additions & 0 deletions bam2bcf_indel.c
View file
Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <assert.h>
#include <ctype.h>
#include <string.h>
Expand Down
2 changes: 2 additions & 0 deletions bam2depth.c
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Expand Up @@ -30,6 +30,8 @@ DEALINGS IN THE SOFTWARE. */
* gcc -g -O2 -Wall -o bam2depth -D_MAIN_BAM2DEPTH bam2depth.c -lhts -lz
*/

#include <config.h>

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_addrprg.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <htslib/sam.h>
#include <htslib/kstring.h>
#include "samtools.h"
Expand Down
2 changes: 2 additions & 0 deletions bam_aux.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <ctype.h>
#include <limits.h>
#include "bam.h"
Expand Down
2 changes: 2 additions & 0 deletions bam_cat.c
View file
Expand Up @@ -34,6 +34,8 @@ and modified to perform concatenation by Chris Saunders on behalf of
Illumina.
*/

#include <config.h>

#include <stdio.h>
#include <stdlib.h>
#include <unistd.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_color.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <ctype.h>
#include "bam.h"

Expand Down
2 changes: 2 additions & 0 deletions bam_flags.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <ctype.h>
#include <string.h>
#include <stdlib.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_import.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <zlib.h>
#include <stdio.h>
#include <string.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_index.c
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Expand Up @@ -24,6 +24,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <htslib/hts.h>
#include <htslib/sam.h>
#include <htslib/khash.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_lpileup.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdlib.h>
#include <stdio.h>
#include <assert.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_mate.c
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Expand Up @@ -24,6 +24,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <assert.h>
#include <stdbool.h>
#include <stdlib.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_md.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <unistd.h>
#include <string.h>
#include <ctype.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_plbuf.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_plcmd.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <math.h>
#include <stdio.h>
#include <stdlib.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_quickcheck.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <htslib/hts.h>
#include <htslib/sam.h>
#include <htslib/bgzf.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_reheader.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdio.h>
#include <stdlib.h>
#include <assert.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_rmdup.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdlib.h>
#include <string.h>
#include <stdio.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_rmdupse.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <math.h>
#include <stdio.h>
#include "bam.h" // for bam_get_library
Expand Down
2 changes: 2 additions & 0 deletions bam_sort.c
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Expand Up @@ -24,6 +24,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdbool.h>
#include <stdlib.h>
#include <ctype.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_split.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <htslib/sam.h>
#include <string.h>
#include <stdio.h>
Expand Down
2 changes: 2 additions & 0 deletions bam_stat.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <unistd.h>
#include <stdint.h>
#include <stdlib.h>
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2 changes: 2 additions & 0 deletions bam_tview.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <regex.h>
#include <assert.h>
#include "bam_tview.h"
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2 changes: 2 additions & 0 deletions bam_tview_html.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <unistd.h>
#include "bam_tview.h"

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2 changes: 2 additions & 0 deletions bamshuf.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <unistd.h>
#include <stdio.h>
#include <stdlib.h>
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2 changes: 2 additions & 0 deletions bamtk.c
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Expand Up @@ -22,6 +22,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <stdio.h>
#include <unistd.h>
#include <fcntl.h>
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2 changes: 2 additions & 0 deletions bedcov.c
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Expand Up @@ -23,6 +23,8 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */

#include <config.h>

#include <zlib.h>
#include <stdio.h>
#include <ctype.h>
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