cram_write_SAM_hdr() now generates M5 strings even when -x (no_ref) is
defined.  This is because although we don't need the MD5 strings when
-x is present for decoding the CRAM, the presence of the M5 tag is
mandatory.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3669 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed the test harness to run with -e and -x scramble parameters.

Bug fixed scramble -x as it was not correctly setting the RI data
series for some tests.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3670 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Removed tiny memory leak of t_stack in thread pool.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3671 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed a buffer read-overrun in COPY_CPF_TO_CPTM macro when there are
no auxiliary tags and the quality string ends at just below 1024 or a
higher power of two.  The macro reads 8 bytes at a time, but we needed
to ensure the buffer is large enough to cope.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3672 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Handle \r\n in SAM files as well as \n.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3673 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1