Commit 6920273f authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

*** empty log message ***

parent d2767d8c
......@@ -14,7 +14,7 @@ use constant { FEATURE_DBID => 0,
FEATURE_END => 3,
FEATURE_STRAND => 4 };
# ----------------------------------------------------------------------
# ======================================================================
# The public interface added by Feature Collection
sub fetch_bins_by_Slice {
......@@ -39,7 +39,7 @@ sub fetch_bins_by_Slice {
return $bins;
}
# ----------------------------------------------------------------------
# ======================================================================
# Specialization of methods in Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
sub _remap {
......@@ -89,7 +89,7 @@ sub _create_feature_fast {
return $feature;
}
# ----------------------------------------------------------------------
# ======================================================================
# Private methods
sub _lightweight {
......@@ -169,7 +169,7 @@ sub _bin_features {
}
if ( $method == 0 ) {
# ----------------------------------------------------------------
# For 'count' and 'density'.
for ( my $bin_index = $start_bin ;
......@@ -180,7 +180,7 @@ sub _bin_features {
}
} elsif ( $method == 1 ) {
# ----------------------------------------------------------------
# For 'indices' and 'index'
for ( my $bin_index = $start_bin ;
......@@ -193,7 +193,7 @@ sub _bin_features {
++$feature_index;
} elsif ( $method == 2 ) {
# ----------------------------------------------------------------
# For 'features' and 'feature'.
for ( my $bin_index = $start_bin ;
......@@ -204,7 +204,7 @@ sub _bin_features {
}
} elsif ( $method == 3 ) {
# ----------------------------------------------------------------
# For 'fractional_count' and 'weight'.
if ( $start_bin == $end_bin ) {
......@@ -237,7 +237,7 @@ sub _bin_features {
} ## end else [ if ( $start_bin == $end_bin)
} elsif ( $method == 4 ) {
# ----------------------------------------------------------------
# For 'coverage'.
my $feature_start = $feature->[FEATURE_START] - $slice_start;
......@@ -296,6 +296,7 @@ sub _bin_features {
if ( $method == 4 ) {
# ------------------------------------------------------------------
# For the 'coverage' method: Finish up by going through @bin_masks
# and sum up the arrays.
......
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