Use calloc instead on the cram_metrics. We weren't initialising all
the fields before and so had uninitialised memory accesses,
potentially leading to poor choices in compression algorithm.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3629 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed two small memory leaks.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3630 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Revert one of the previous memory leaks as it breaks multi-threading.
I need to find a more suitable way to solve this. The memory leak is
back, but it's tiny; essentially leaking the last (empty) container.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3631 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Placed the branch in the proper subdirectory.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3632 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Better fix for container memory leak. Now parses valgrind in threaded
and non-threaded mode.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3633 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Made cram_to_bam() honour the required_fields SAM_QNAME check.
This substantially speeds up scram_flagstat by 50-130%.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3634 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Improved printing of external blocks.


git-svn-id: svn://svn.code.sf.net/p/staden/code/io_lib@3635 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1