added missing method
fix synopsis
sizes() now allows for a Bio::Restriction::EnzymeI (with tests), fixes #3157
moved functions to Bio::SearchIO so they can be used generically, though completely untested, refs #2247
add maintenance/find_mod_deps.pl, which lists (non-core) dependencies of the whole distribution, or just the set of files and dirs specified at the command line
* 'use vars' -> our
* run-time modification of @ISA is extremely evil and points to a problem
that should be fixed in other ways.  Commenting this out still passes
tests; I openly implore anyone who used such evilness to please find
a better fix
* add tests that check trucated sequence length matches the qual data
length, fixes #2891
* note that the raw FASTQ string is NOT stored in the instances
Allow falling back to any strigified Bio::AnnotationI for 'gene_name'
(along with tests), fixes #3153.
rewrote usage script

Comment by rbuels: actually, it's more of a refactor and correction of
the bp_seqfeature_load.PLS usage message.
fix test fail from bad file name
comment out overzealous error checking, which caused some EMBL files to not parse, fixes #3158
make sure short params don't conflict, make them explicit
enable fast loading with namespaces; empty tables were being generated
that had concatenated table names via _qualify() (e.g.
volvox_volvox_feature); this fix checks for the presence of the
namespace just in case and returns it w/o modification if it is found
removed a few tests that can return ambigous results depending on a sort
fix for bug #3198
adding test for bug #3039. Copied over manually from topic/bug3039. Current code on master passes this test, so it must have been fixed during the refactor.
find_mod_deps.pl maint script should skip nonexistent files
add -B option to find_mod_deps, which prints the deps in Build.PL format
add -M option to find_mod_deps for Module::Install output format
sigh, can't resist adding Dist::Zilla format for completeness.