Script to examine exons before and after projection. Designed to work with Anacode Support objects, so jiggery pokery with paths needed to get started. Use with arguments similar to the Assembly Mapping pipeline.

Needs more POD.

Attempt to speed up. Previous use of Algorithm::Diff was prohibitively slow, so attempting to use bitmasking on simple cases to go 10x faster on the easy cases.

Added missing parameter to allow secondary database password. Otherwise it defaults to none and fails.

Removed reference to $SERVERROOT because it's just confusing and makes things harder. Just have your Perl5Lib properly set.

new script to fix mapping coordinates in asm_start, asm_end columns; don't merge or bridge gaps as this is done ordering by cmp_start in fix_cmp_overlaps.pl

don't limit seq_region to chromosomes, so the script can be used to fix overlaps in mappings between other coord_systems

changed mapping percentage calculation per alignment length bin to use non-N sequence length like the total mapping percentage per chromosome