TEST_MAIN2 version of main() for testing on larger inputs, read from
stdin rather than argv[1] as a string.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3729 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1
Fixed memory leak and slow down caused by last patch to STR finder
calling.

Added seed_malign_region() to perform a rudimentary screen on the
heterozygous consensus to only request realignment in regions that are
heterozygous in nature.

TODO: Make this an optional 3 way - all regions, all hets, het indel only.


git-svn-id: svn://svn.code.sf.net/p/staden/code/staden/trunk@3730 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1