Fixes for bugs in map_reads, import_reads and calculate_consensus_bit_het.

Fix various bugs:

 Attempt to read a closed filehandle in MapReads_run (map_reads.tcl).

 Not setting link_pairs parameter in tcl_import_reads (newgap5_cmds.c).

 Failure to resize s->pad in sam_add_seq, leading to a buffer overflow if
 enough pads get added (sam_index.c).

 Reading past the end of a sequence in calculate_consensus_bit_het if the
 right clip point is past the end.  This shouldn't happen, but databases do
 exist with clipping broken in this way.



git-svn-id: https://staden.svn.sourceforge.net/svnroot/staden/staden/trunk@3146 ba6f2710-ca9f-427c-89d3-5bf716dbc8e1