CHANGES IN VERSION 3.8.0
------------------------

- No changes in this version.


CHANGES IN VERSION 3.6.0
------------------------

- No significant changes in this version.


CHANGES IN VERSION 3.4.0
------------------------

- No significant changes in this version.


CHANGES IN VERSION 3.2.0
------------------------

- No significant changes in this version.


CHANGES IN VERSION 3.0.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Update htslib to 1.18 (was 1.15.1)


CHANGES IN VERSION 2.2.0
-------------------------

- No significant changes in this version.


CHANGES IN VERSION 2.0.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Update htslib to 1.15.1 (was 1.7)


CHANGES IN VERSION 1.28.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Acknowledge site-wide or user-specified Makevars file if present.


CHANGES IN VERSION 1.26.0
-------------------------

- No significant changes in this version.


CHANGES IN VERSION 1.24.0
-------------------------

- No significant changes in this version.


CHANGES IN VERSION 1.22.0
-------------------------

- No significant changes in this version.


CHANGES IN VERSION 1.20.0
-------------------------

- No significant changes in this version.


CHANGES IN VERSION 1.18.0
-------------------------

NEW FEATURES

    o Compile HTSlib with libcurl enabled

    o Support an installation path that contains whitespaces

SIGNIFICANT USER-VISIBLE CHANGES

    o Switch from dynamic to static linking on all Unix-like systems (see
      commit db1d8e17)

    o Package now requires libbz2 & liblzma & libcurl (with header files),
      and GNU make. This is declared in new SystemRequirements field.

BUG FIXES

    o Use preprocessor flag -D_FILE_OFFSET_BITS=64. This addresses nasty
      problem with big files that get truncated on Windows. See
      https://support.bioconductor.org/p/124568/

    o Don't overwrite CPPFLAGS, CFLAGS, or LDFLAGS values set in
      ${R_HOME}/etc/Makeconf on Linux or Mac


CHANGES IN VERSION 1.16.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Include various additional files from Samtools 1.7: bam_aux.c,
      bam_endian.h, and bam_cat.c

    o Add C function faidx_fetch_seq_forced_lower() to the HTSlib code.
      This is an alternative to HTSlib C function faidx_fetch_seq(), with the
      following difference: if coordinates are outside the actual sequence,
      write N's, rather than adjusting the start,end.
      Used in the seqbias package (and originally written by seqbias' author
      and maintainer, Daniel Jones).

BUG FIXES

    o Fix long-standing kvsprintf() bug on Windows. This low-level bug was
      responsible for breaking "scan_bcf_header" .Call entry point in
      Rsamtools, which in turn was responsible for the infamous
      'invalid class "VCFHeader" object' bug in VariantAnnotation::readVcf().

    o Fix for Solaris: Do not build standalone executables (e.g. bgzip, tabix,
      etc...). They're not needed and seem to cause problems on Solaris.


CHANGES IN VERSION 1.14.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o Include the test data files from htslib-1.7/test
      For convenience, the .sam, .bam, .vcf, .bcf, .cram, .fa, .fa.fai, .gff,
      and .bed files located under htslib-1.7/test now are also included in
      the package (under ${R_PACKAGE_DIR}/testdata). They can be accessed with
      something like:
          system.file(package="Rhtslib", "testdata", "ce#1.sam")
      or:
          system.file(package="Rhtslib", "testdata", "tabix", "vcf_file.vcf")

    o Change installation folder of htslib header files. HTSlib header files
      now get installed in ${R_PACKAGE_DIR}/include/htslib instead of
      ${R_PACKAGE_DIR}/include so C/C++ code that needs to include them
      now should use directives like:

          #include "htslib/hts.h"
          #include "htslib/sam.h"
          #include "htslib/bgzf.h"

      instead of:

          #include "hts.h"
          #include "sam.h"
          #include "bgzf.h"

    o Include various .h and .c files from Samtools 1.7 (in
      ${R_PACKAGE_DIR}/include). These files come from the top-level folder
      of the Samtools source tree. See Rhtslib/inst/include/README for more
      information.

    o Include textutils_internal.h and hts_internal.h from HTSlib 1.7 (in
      ${R_PACKAGE_DIR}/include). These files come from the top-level folder
      of the HTSlib source tree.

    o Add C function faidx_fetch_seq2() to the HTSlib code. This is an
      alternative to HTSlib C function faidx_fetch_seq(), with the following
      differences:
        1) writes the incoming sequence to user-supplied 'out' buffer,
        2) doesn't write the terminating null byte ('\0'),
        3) properly handles 0-length sequences,
        4) returns the number of bytes written; -1 on failure.
      It will be used in Rsamtools::scanFa() when Rsamtools gets migrated
      to Rhtslib. It allows the incoming sequences to be loaded directly
      into the DNAStringSet object to return.

    o Add C function hts_idx_get_n() to the HTSlib code. This function will
      be used in Rsamtools::idxstatsBam() when Rsamtools gets migrated
      to Rhtslib.

BUG FIXES

    o Simplify PKG_LIBS on Mac. There should be no need to use linker options
      -lz -lm -lbz2 -llzma -lcurl and -lpthread on Mac when making the package
      shared object because we link against **static** library libhts.a on
      this platform.


CHANGES IN VERSION 1.12.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o The HTSlib C library was updated from version 1.1 to version 1.7.

