New upstream version 1.14.11

# Everything generated from ./bootstrap (autoconf)

Makefile.in

aclocal.m4

autom4te.cache

compile

config.guess

config.sub

configure

depcomp

install-sh

io_lib/Makefile.in

io_lib_config.h.in

ltmain.sh

missing

progs/Makefile.in

test-driver

tests/Makefile.in

# Skip local build sub-directories per OS.

build.*

language: c

compiler: gcc

script: ./bootstrap; ./configure && make && (make check || (cat tests/test-suite.log; false))

Version 1.14.11 (16th October 2018)

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

Updates:

* CRAM: http(s) queries now honour redirects.

  The User-Agent header is also set, which is necessary in some

  proxies.

Bug fixes:

* CRAM: fix to major range query bug introduced in 1.14.10.

* CRAM: more bug fixing on range queries when multi-threading (EOF

  detection).

* The test harness now works correctly in bourne shell, without

  using bashisms.

Version 1.14.10 (26th September 2018)

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

Updates:

* BAM: Libdeflate support (https://github.com/ebiggers/libdeflate).

  This library is significantly faster than zlib, so it is a good

  alternative to the Cloudflare and/or Intel libraries.

  Configure using --with-libdeflate=/dir/to/deflate/install

* CRAM *EXPERIMENTAL*: Added custom quality and identifier codecs.

  Also added the ability to use libbsc as a general purpose codec.

  These are NOT OFFICIAL and so not enabled by default (version 3.0).

  However as a technology demonstration only, they are available with

  scramble -V3.1 or -V4.0 for evaluation and to promote discussion on

  future CRAM formats.  Do not use these on production data.

  Implementations of the codecs and CRAM version 4.0 layout are liable

  to change without prior warning.

* CRAM: name sorted files now automatically switch to non-ref mode.

Bug fixes:

* CRAM: Considerable fixes to multi-threading.

  - Using more than 1 slice per container with threading now works.

  - Removal of race conditions when using CRAM_OPT_REQUIRED_FIELDS.

  - Combinations of ref and no-ref mode in adjacent containers.

  - Other misc. threading bugs.

* Corrected end-of-range check in some scenarios.

* CRAM: bug fix to index creation when a slice contains exactly one

  alignment.

* SAM: fixed parsing of illegal sequence characters (eg "Z").

  These are now treated as "N" and not "=".

* BAM/SAM: protect against out of bound CIGAR operations.

* CRAM: hardening of rANS codec against malicious input.

  Also fixed a very rare frequency renormalisation case.

* CRAM: fix with range queries used in conjuction with turning off

  sequence retrieval (via CRAM_OPT_REQUIRED_FIELDS).

* Improved test harness for Windows and some header file problems.

* Fixed bgzip on big endian systems. (Debian bugs 876839, 876840)

Version 1.14.9 (9th February 2017)

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

//Technically this is provided by Winsock2.h

//https://msdn.microsoft.com/en-us/library/windows/desktop/ms740560%28v=vs.85%29.aspx?f=255&MSPPError=-2147217396

typedef struct timeval {

  long tv_sec;

  long tv_usec;

} timeval;