Commit [r3641] Maximize Restore History

1. Added an extra depadding option to Export Contigs; reference sequence

positions (in addition to the old padded and unpadded consensus mode).
The purpose of this is to allow tg_index to import a sam/bam/cram, run
tools like Shuffle Pads on it, and then export back in the same
coordinate system as the original BAM.

It is not expected to work after joining and breaking has been
applied, although it needs better error handling to cope with this
more gracefully.

Updated the padded_to_reference_array() function to aid this work.

2. Fixed a bug in create_ref_seq(). It was producing incorrect .fai
files for contigs that do not start at base 1.

3. Fixed memory corruption in sam_add_seq() caused when using
excessive padding in CIGAR ops during tg_index.

4. Bug fix to contig_insert_base_common() when manipulating the
REF_POS markers. It wasn't coping correctly with this in some
complemented scenarios and with nbases > 1.

jkbonfield 2014-05-01

changed /staden/trunk/src/gap5/tg_contig.c
changed /staden/trunk/src/gap5/gap5_cmd.tcl
changed /staden/trunk/src/gap5/editor_view.c
changed /staden/trunk/src/gap5/tg_contig.h
changed /staden/trunk/src/gap5/sam_pileup.h
changed /staden/trunk/src/gap5/export_contigs.c
changed /staden/trunk/src/gap5/export_contigs.tcl
changed /staden/trunk/src/gap5/sam_index.c
/staden/trunk/src/gap5/tg_contig.c Diff Switch to side-by-side view
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/staden/trunk/src/gap5/gap5_cmd.tcl Diff Switch to side-by-side view
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/staden/trunk/src/gap5/editor_view.c Diff Switch to side-by-side view
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/staden/trunk/src/gap5/tg_contig.h Diff Switch to side-by-side view
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/staden/trunk/src/gap5/sam_pileup.h Diff Switch to side-by-side view
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/staden/trunk/src/gap5/export_contigs.c Diff Switch to side-by-side view
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/staden/trunk/src/gap5/export_contigs.tcl Diff Switch to side-by-side view
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/staden/trunk/src/gap5/sam_index.c Diff Switch to side-by-side view
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