New upstream version 0.0+git20200125.51bc9725+dfsg

     o (in 36x2) Fixed problem with -maxIntron set to non-default value on protein query.

     o (in 36x3) Added ipv6 support.

     o (in 36x4) Added _alt support.

     o (in 36x5) If ipv6 disabled, retries with ipv4-only socket.

36:

     o (in 35x1) added repMatch default values for tileSizes 16 to 18 in genoFind.c

Basic Installation

==================

To build and install HTSlib, 'cd' to the htslib-1.x directory containing

the package's source and type the following commands:

    ./configure

    make

    make install

The './configure' command checks your build environment and allows various

optional functionality to be enabled (see Configuration below).  If you

don't want to select any optional functionality, you may wish to omit

configure and just type 'make; make install' as for previous versions

of HTSlib.  However if the build fails you should run './configure' as

it can diagnose the common reasons for build failures.

The 'make' command builds the HTSlib library and and various useful

utilities: bgzip, htsfile, and tabix.  If compilation fails you should

run './configure' as it can diagnose problems with your build environment

that cause build failures.

The 'make install' command installs the libraries, library header files,

utilities, several manual pages, and a pkgconfig file to /usr/local.

The installation location can be changed by configuring with --prefix=DIR

or via 'make prefix=DIR install' (see Installation Locations below).

Configuration

=============

By default, './configure' examines your build environment, checking for

requirements such as the zlib development files, and arranges for a plain

HTSlib build.  The following configure options can be used to enable

various features and specify further optional external requirements:

--enable-plugins

    Use plugins to implement exotic file access protocols and other

    specialised facilities.  This enables such facilities to be developed

    and packaged outwith HTSlib, and somewhat isolates HTSlib-using programs

    from their library dependencies.  By default, any enabled pluggable

    facilities (such as iRODS and libcurl file access) are built directly

    within HTSlib.

--with-plugin-dir=DIR

    Specifies the directory into which plugins built while building HTSlib

    should be installed; by default, LIBEXECDIR/htslib.

--with-plugin-path=DIR:DIR:DIR...

    Specifies the list of directories that HTSlib will search for plugins.

    By default, only the directory specified via --with-plugin-dir will be

    searched; you can use --with-plugin-path='DIR:$(plugindir):DIR' and so

    on to cause additional directories to be searched.

--with-irods[=DIR]

    Specifies the location of the iRODS client library to use to enable

    access to data objects stored in iRODS (<http://irods.org/>) via file

    paths like 'irods:DATAOBJ'.  DIR is the base of an iRODS source tree

    such that the library is present as DIR/lib/core/obj/libRodsAPI.* and

    headers are present under DIR/lib/api/include and so on.  If '=DIR' is

    omitted, $IRODS_HOME will be used as a base directory.

--enable-libcurl

    Use libcurl (<http://curl.haxx.se/>) to implement network access to

    remote files via FTP, HTTP, HTTPS, S3, etc.  By default, HTSlib uses

    its own simple networking code to provide access via FTP and HTTP only.

The configure script also accepts the usual options and environment variables

for tuning installation locations and compilers: type './configure --help'

for details.  For example,

    ./configure CC=icc --prefix=/opt/icc-compiled

would specify that HTSlib is to be built with icc and installed into bin,

lib, etc subdirectories under /opt/icc-compiled.

Installation Locations

======================

By default, 'make install' installs HTSlib libraries under /usr/local/lib,

HTSlib header files under /usr/local/include, utility programs under

/usr/local/bin, etc.  (To be precise, the header files are installed within

a fixed 'htslib' subdirectory under the specified .../include location.)

You can specify a different location to install HTSlib by configuring

with --prefix=DIR or specify locations for particular parts of HTSlib by

configuring with --libdir=DIR and so on.  Type './configure --help' for

the full list of such install directory options.

Alternatively you can specify different locations at install time by

typing 'make prefix=DIR install' or 'make libdir=DIR install' and so on.

Consult the list of prefix/exec_prefix/etc variables near the top of the

Makefile for the full list of such variables that can be overridden.

You can also specify a staging area by typing 'make DESTDIR=DIR install',

possibly in conjunction with other --prefix or prefix=DIR settings.

For example,

    make DESTDIR=/tmp/staging prefix=/opt

would install into bin, lib, etc subdirectories under /tmp/staging/opt.

[Files in this distribution outwith the cram/ subdirectory are distributed

according to the terms of the following MIT/Expat license.]

The MIT/Expat License

Copyright (C) 2012-2014 Genome Research Ltd.

Permission is hereby granted, free of charge, to any person obtaining a copy

of this software and associated documentation files (the "Software"), to deal

in the Software without restriction, including without limitation the rights

to use, copy, modify, merge, publish, distribute, sublicense, and/or sell

copies of the Software, and to permit persons to whom the Software is

furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER

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.

[Files within the cram/ subdirectory in this distribution are distributed

according to the terms of the following Modified 3-Clause BSD license.]

The Modified-BSD License

Copyright (C) 2012-2014 Genome Research Ltd.

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice,

   this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice,

   this list of conditions and the following disclaimer in the documentation

   and/or other materials provided with the distribution.

3. Neither the names Genome Research Ltd and Wellcome Trust Sanger Institute

   nor the names of its contributors may be used to endorse or promote products

   derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS IS"

AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH LTD OR ITS CONTRIBUTORS BE LIABLE

FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR

SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER

CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

[The use of a range of years within a copyright notice in this distribution

should be interpreted as being equivalent to a list of years including the

first and last year specified and all consecutive years between them.

For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,

2011-2012" should be interpreted as being identical to a notice that reads

"Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice

that reads "Copyright (C) 2005-2012" should be interpreted as being identical

to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,

2011, 2012".]

Noteworthy changes in release 1.3  (15 December 2015)

* Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP

  and FTP, when HTSlib is configured to use libcurl for network file access

  rather than the included basic knetfile networking.

* HTSlib can be built to use remote access hFILE backends (such as iRODS

  and libcurl) via a plugin mechanism.  This allows other backends to be

  easily added and facilitates building tools that use HTSlib, as they

  don't need to be linked with the backends' various required libraries.

* fai_build() and samtools faidx now accept initial whitespace in ">"

  headers (e.g., "> chr1 description" is taken to refer to "chr1").

* tabix --only-header works again (was broken in 1.2.x; #249).

* HTSlib's configure script and Makefile now fully support the standard

  convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden

  as needed.  Previously the Makefile listened to $(LDLIBS) instead; if you

  were overriding that, you should now override LIBS rather than LDLIBS.

* Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296.

Noteworthy changes in release 1.2.1  (3 February 2015)

* Reinstated hts_file_type() and FT_* macros, which were available until 1.1

  but briefly removed in 1.2.  This function is deprecated and will be removed

  in a future release -- you should use hts_detect_format() etc instead

Noteworthy changes in release 1.2  (2 February 2015)

* HTSlib now has a configure script which checks your build environment

  and allows for selection of optional extras.  See INSTALL for details

* By default, reference sequences are fetched from the EBI CRAM Reference

  Registry and cached in your $HOME cache directory.  This behaviour can

  be controlled by setting REF_PATH and REF_CACHE enviroment variables

  (see the samtools(1) man page for details)

* Numerous CRAM improvements:

  - Support for CRAM v3.0, an upcoming revision to CRAM supporting

    better compression and per-container checksums

  - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks)

  - Non-standard values for PNEXT and TLEN fields are now preserved

  - hts_set_fai_filename() now provides a reference file when encoding

  - Generated read names are now numbered from 1, rather than being

    labelled 'slice:record-in-slice'

  - Multi-threading and speed improvements

* New htsfile command for identifying file formats, and corresponding

  file format detection APIs

* New tabix --regions FILE, --targets FILE options for filtering via BED files

* Optional iRODS file access, disabled by default.  Configure with --with-irods

  to enable accessing iRODS data objects directly via 'irods:DATAOBJ'

* All occurences of 2^29 in the source have been eliminated, so indexing

  and querying against reference sequences larger than 512Mbp works (when

  using CSI indices)

* Support for plain GZIP compression in various places

* VCF header editing speed improvements

* Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table)

* Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1.

  Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually

  faidx_fetch_nseq() will be deprecated and removed [#156]

* Fixed bugs #141, #152, #155, #158, #159, and various memory leaks