New upstream version 1.7

# branches to build

branches:

    # Whitelist

    only:

      - develop

    # Blacklist

    except:

      - gh-pages

LDFLAGS  =

LIBS     =

LZ4DIR   = ./lz4

LZ4_CPPFLAGS = -I$(LZ4DIR)

LZ4_LDFLAGS  = -L$(LZ4DIR)

LOBJS=      bam_aux.o bam.o bam_import.o sam.o \

            sam_header.o bam_plbuf.o

AOBJS=      bam_index.o bam_plcmd.o sam_view.o \

            cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \

            faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \

            bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \

            bam_quickcheck.o bam_addrprg.o bam_markdup.o

            bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o

LZ4OBJS  =  $(LZ4DIR)/lz4.o

prefix      = /usr/local

exec_prefix = $(prefix)

all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)

ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)

ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)

ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(LZ4_CPPFLAGS) $(CPPFLAGS)

ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LZ4_LDFLAGS) $(LDFLAGS)

ALL_LIBS     = -lz $(LIBS)

# Usually config.mk and config.h are generated by running configure

.c.o:

	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<

LIBST_OBJS = sam_opts.o sam_utils.o

libbam.a:$(LOBJS)

	$(AR) -csru $@ $(LOBJS)

samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread

samtools: $(AOBJS) $(LZ4OBJS) libbam.a libst.a $(HTSLIB)

	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) $(LZ4OBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread

# For building samtools and its test suite only: NOT to be installed.

libst.a: $(LIBST_OBJS)

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)

tmp_file_h = tmp_file.h $(htslib_sam_h) $(LZ4DIR)/lz4.h

bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h

bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_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)

bam_markdup.o: bam_markdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)

bam_markdup.o: bam_markdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h) $(tmp_file_h)

tmp_file.o: tmp_file.c config.h $(tmp_file_h)

# test programs

	-cd test/mpileup && rm -f FAIL-*.out* PASS-*.out* anomalous.[bc]*am indels.[bc]*am mpileup.*.[cs]*am mpileup.*.crai overlap50.[bc]*am expected/1.out xx#depth*.bam*

mostlyclean: testclean

	-rm -f *.o misc/*.o test/*.o test/*/*.o version.h

	-rm -f *.o misc/*.o test/*.o test/*/*.o version.h $(LZ4OBJS)

clean: mostlyclean

	-rm -f $(PROGRAMS) libbam.a libst.a $(MISC_PROGRAMS) $(TEST_PROGRAMS)

Release 1.7 (26th January 2018)

--------------------

* HTSlib, and so samtools, now support BAMs which include CIGARs with more

  than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8).

* samtools quickcheck will now write a warning to stderr if it finds

  any problems.  These messages can be suppressed with a new `-q` option.

* samtools markdup can now mark supplementary alignments of reads where

  the primary alignment is found to be a duplicate.  Supplementary marking

  can be turned on by passing the `-S` option to markdup.  When this

  option is enabled, all the alignment data will be written to a temporary

  file so that supplementary alignments that occur before a duplicated

  primary can be correctly marked in the final output.  The location

  of this temporary file can be influenced using the new `-T` option.

* samtools view now supports HTSlib's new multi-region iterator.

  This can be enabled by passing the `-M` option to view.  When using

  this option:

  - The BED filter (`-L` option) will use the index to skip through the file

  - Reads from overlapping regions will only be output once

* samtools bedcov will now ignore BED comment and header lines (#571; thanks

  to Daniel Baker).

* samtools collate now updates the @HD SO: and GO: tags, and sort will

  remove a GO: tag if present.  (#757; reported by Imran Haque).

* Bug-fixes:

 - maq2sam now checks for input files that end early.  (#751; patch supplied

   by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.)

 - Fixed incorrect check when looking up header tags that could lead

   to a crash in samtools stats. (#208; thanks to Dave Larson.)

 - Fixed bug in samtools fastq `-O` option where it would fail if

   the OQ tag in the input file had an unexpected type. (#758;

   reported by Taejeong Bae)

 - The MD5 calculations in samtools dict and md5fa did not handle

   non-alphabetic characters in the same way as the CRAM MD5 function.

   They have now been updated to match. (#704; reported by Chris Norman).

 - Fix possible infinite loop in samtools targetcut.

 - Building bam_tview_curses should no longer fail if a curses header file

   cannot be found.

Release 1.6 (28th September 2017)

--------------------

The typical simple case of building Samtools using the HTSlib bundled within

this Samtools release tarball is done as follows:

    cd .../samtools-1.6 # Within the unpacked release directory

    cd .../samtools-1.7 # Within the unpacked release directory

    ./configure

    make

installation using the HTSlib bundled within this Samtools release tarball,

and building the various HTSlib utilities such as bgzip is done as follows:

    cd .../samtools-1.6 # Within the unpacked release directory

    cd .../samtools-1.7 # Within the unpacked release directory

    ./configure --prefix=/path/to/location

    make all all-htslib

    make install install-htslib

  @copyright Genome Research Ltd.

 */

#define BAM_VERSION "1.6"

#define BAM_VERSION "1.7"

#include <stdint.h>

#include <stdlib.h>