quick fix for get()ing models with config items in CQID
Use the profile item test factory module.
fix inner loop naming for clarity
Merge pull request #26 from acoffman/master

quick fix for get()ing models with config items in CQID
factor out common writer code from Genome::File::*::Writer

all code is now in a common base class Genome::File::TypedWriter. None
of the readers (Vcf, Vep, BedPe) make any customizations, but the
original writer classes still exist (and just inherit from the base) for
compatibility.
rename G:F:TypedStream to G:F:TypedReader

there's a TypedWriter now; this naming makes more sense.
add G:F:Breakdancer

for breakdancer file i/o
add new_from_fields() to G:F:BedPe::Entry
add custom_by_name method to bedpe object

my $idx = $entry->{header}->custom_field_index("foo");
$entry->{custom}[$idx];

is now

$entry->custom_by_name("foo");
add lib_read_count method to breakdancer entry object

returns the number of reads originating from the given library
add G:F:Breakdancer::ToBedPe

to convert breakdancer entries to bedpe.