diff --git a/.buildinfo b/.buildinfo index 08b63d5..03c4c1f 100644 --- a/.buildinfo +++ b/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: d602bcf906c7a4a36615613d569d886e +config: 04ee4c223e16b4397ddda934d50f4909 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/_modules/index.html b/_modules/index.html index 4785abd..cfe82d4 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -5,7 +5,7 @@ - Overview: module code - IRanges 0.0.1 documentation + Overview: module code - IRanges 0.1.0 documentation @@ -122,7 +122,7 @@
-
IRanges 0.0.1 documentation
 +
IRanges 0.1.0 documentation
@@ -145,7 +145,7 @@
- IRanges 0.0.1 documentation + IRanges 0.1.0 documentation
@@ -230,7 +231,7 @@

All modules for which code is available

-
+ diff --git a/_modules/iranges/IRanges.html b/_modules/iranges/IRanges.html index 82a553c..ce8a25e 100644 --- a/_modules/iranges/IRanges.html +++ b/_modules/iranges/IRanges.html @@ -5,7 +5,7 @@ - iranges.IRanges - IRanges 0.0.1 documentation + iranges.IRanges - IRanges 0.1.0 documentation @@ -122,7 +122,7 @@
-
IRanges 0.0.1 documentation
 +
IRanges 0.1.0 documentation
@@ -145,7 +145,7 @@
- IRanges 0.0.1 documentation + IRanges 0.1.0 documentation @@ -198,13 +198,63 @@

Source code for iranges.IRanges

 from copy import deepcopy
-from typing import List, Optional, Sequence, Union
+from itertools import chain
+from typing import List, Literal, Optional, Sequence, Tuple, Union
 from warnings import warn
 
 import biocutils as ut
 from biocframe import BiocFrame
-from biocgenerics import combine_rows, combine_seqs, format_table, show_as_cell
-from numpy import array, get_printoptions, int32, ndarray
+from biocgenerics import combine_rows, combine_seqs, show_as_cell
+from numpy import array, clip, int32, ndarray, printoptions, where, zeros
+
+from .interval import calc_gap_and_overlap, create_np_interval_vector
+
+__author__ = "Aaron Lun, Jayaram Kancherla"
+__copyright__ = "LTLA, jkanche"
+__license__ = "MIT"
+
+
+

+[docs]
+class IRangesIter:
+    """An iterator to :py:class:`~iranges.IRanges.IRanges`.
+
+    Args:
+        obj (IRanges): Object to iterate.
+    """
+
+    def __init__(self, obj: "IRanges") -> None:
+        """Initialize the iterator.
+
+        Args:
+            obj (IRanges): Source object to iterate.
+        """
+        self._iranges = obj
+        self._current_index = 0
+
+

+[docs]
+    def __iter__(self):
+        return self

+
+
+

+[docs]
+    def __next__(self):
+        if self._current_index < len(self._iranges):
+            iter_row_index = (
+                self._iranges.names[self._current_index]
+                if self._iranges.names is not None
+                else None
+            )
+
+            iter_slice = self._iranges.get_row(self._current_index)
+            self._current_index += 1
+            return (iter_row_index, iter_slice)
+
+        raise StopIteration

+

+
 
 
 

@@ -756,16 +806,9 @@ 
Source code for iranges.IRanges
 

 [docs]
     def __repr__(self) -> str:
-        opt = get_printoptions()
-        old_threshold = opt["threshold"]
-        old_edgeitems = opt["edgeitems"]
-
-        try:
-            opt["threshold"] = 50
-            opt["edgeitems"] = 3
+        with printoptions(threshold=50, edgeitems=3):
             message = "IRanges(start=" + repr(self._start)
             message += ", width=" + repr(self._width)
-
             if self._names:
                 message += ", names=" + ut.print_truncated_list(self._names)
 
@@ -773,12 +816,9 @@ 
Source code for iranges.IRanges
                 message += ", mcols=" + repr(self._mcols)
 
             if len(self._metadata):
-                message += ", metadata=" + repr(self._metadata)
+                message += ", metadata=" + ut.print_truncated_dict(self._metadata)
 
             message += ")"
-        finally:
-            opt["threshold"] = old_threshold
-            opt["edgeitems"] = old_edgeitems
 
         return message

 
@@ -807,19 +847,23 @@ 
Source code for iranges.IRanges
                 indices = [0, 1, 2, nranges - 3, nranges - 2, nranges - 1]
                 insert_ellipsis = True
 
-            if self._names is not None:
-                raw_floating = ut.subset(self._names, indices)
-            else:
-                raw_floating = ["[" + str(i) + "]" for i in indices]
+            raw_floating = ut.create_floating_names(self._names, indices)
             if insert_ellipsis:
                 raw_floating = raw_floating[:3] + [""] + raw_floating[3:]
             floating = ["", ""] + raw_floating
 
             columns = []
-            for prop in ["start", "end", "width"]:
-                data = getattr(self, "get_" + prop)()
-                showed = show_as_cell(data, indices)
-                header = [prop, "<" + type(data).__name__ + ">"]
+
+            sub_start = self._start[indices]
+            sub_width = self._width[indices]
+            sub_end = sub_start + sub_width
+            for prop, val in [
+                ("start", sub_start),
+                ("end", sub_end),
+                ("width", sub_width),
+            ]:
+                header = [prop, "<" + ut.print_type(val) + ">"]
+                showed = show_as_cell(val, range(len(val)))
                 if insert_ellipsis:
                     showed = showed[:3] + ["..."] + showed[3:]
                 columns.append(header + showed)
@@ -831,26 +875,28 @@ 
Source code for iranges.IRanges
                 for col in self._mcols.get_column_names():
                     data = self._mcols.column(col)
                     showed = show_as_cell(data, indices)
-                    header = [col, "<" + type(data).__name__ + ">"]
-                    minwidth = max(40, len(header[0]), len(header[1]))
-                    for i, y in enumerate(showed):
-                        if len(y) > minwidth:
-                            showed[i] = y[: minwidth - 3] + "..."
+                    header = [col, "<" + ut.print_type(data) + ">"]
+                    showed = ut.truncate_strings(
+                        showed, width=max(40, len(header[0]), len(header[1]))
+                    )
                     if insert_ellipsis:
                         showed = showed[:3] + ["..."] + showed[3:]
                     columns.append(header + showed)
 
-            output += format_table(columns, floating_names=floating)
+            output += ut.print_wrapped_table(columns, floating_names=floating)
             added_table = True
 
         footer = []
         if len(self._metadata):
             footer.append(
-                "metadata ("
+                "metadata("
                 + str(len(self._metadata))
                 + "): "
                 + ut.print_truncated_list(
-                    list(self._metadata.keys()), sep=" ", include_brackets=False
+                    list(self._metadata.keys()),
+                    sep=" ",
+                    include_brackets=False,
+                    transform=lambda y: y,
                 )
             )
         if len(footer):
@@ -901,6 +947,1248 @@ 
Source code for iranges.IRanges
             metadata=deepcopy(self._metadata, memo),
             validate=False,
         )

+
+
+

+[docs]
+    def get_row(self, index_or_name: Union[str, int]) -> "IRanges":
+        """Access a row by index or row name.
+
+        Args:
+            index_or_name (Union[str, int]): Integer index of the row to access.
+
+                Alternatively, you may provide a string specifying the row name to access,
+                only if :py:attr:`~iranges.IRanges.IRanges.names` are available.
+
+        Raises:
+            ValueError:
+                If ``index_or_name`` is not in row names.
+                If the integer index is greater than the number of rows.
+            TypeError:
+                If ``index_or_name`` is neither a string nor an integer.
+
+        Returns:
+            IRanges: A sliced IRanges object
+        """
+
+        if not isinstance(index_or_name, (int, str)):
+            raise TypeError("`index_or_name` must be either an integer index or name.")
+
+        return self[index_or_name]

+
+
+

+[docs]
+    def __iter__(self) -> IRangesIter:
+        """Iterator over intervals."""
+        return IRangesIter(self)

+
+
+    ############################
+    #### iter range methods ####
+    ############################
+
+

+[docs]
+    def clip_intervals(
+        self, shift: int = 0, width: Optional[Union[int, List[int]]] = None
+    ) -> "IRanges":
+        """Clip intervals. Starts are always clipped to positive interval ranges (1, Inf).
+
+        If ``width`` is specified, the intervals are clipped to (1, width).
+
+        Args:
+            shift (int, optional): Shift all starts before clipping. Defaults to 0.
+            width (Union[int, List[int]], optional): Clip width of each interval. Defaults to None.
+
+        Returns:
+            IRanges: A ``IRanges`` object, with the clipped intervals.
+        """
+
+        _clipped_starts = []
+        _clipped_widths = []
+        _clipped_names = []
+
+        counter = 0
+        for name, val in self:
+            _start = val.start[0]
+            _width = val.width[0]
+
+            if shift > 0:
+                _start += shift
+
+            if width is not None:
+                if not isinstance(width, int):
+                    raise TypeError("'width' must be either an integer or a vector.")
+
+                if _start + _width > width:
+                    _width = width - _start
+
+            counter += 1
+
+            if _start < 1:
+                _start = 1
+                _width = val.end[0] - _start
+
+            _end = _start + _width
+            if _end < 1:
+                continue
+
+            _clipped_starts.append(_start)
+            _clipped_widths.append(_width)
+            _clipped_names.append(name if name is not None else str(counter - 1))
+
+        if all(x is None for x in _clipped_names):
+            _clipped_names = None
+
+        return IRanges(_clipped_starts, _clipped_widths, names=_clipped_names)

+
+
+

+[docs]
+    def coverage(
+        self, shift: int = 0, width: Optional[int] = None, weight: Union[int, float] = 1
+    ) -> ndarray:
+        """Calculate coverage, for each position, counts the number of intervals that cover it.
+
+        Args:
+            shift (int, optional): Shift all intervals. Defaults to 0.
+            width (int, optional): Restrict the width of all intervals. Defaults to None.
+            weight (Union[int, float], optional): Weight to use. Defaults to 1.
+
+        Raises:
+            - If 'weight' is not a number.
+            - If 'width' is not a number.
+
+        Returns:
+            ndarray:  A numpy array with the coverage vector.
+        """
+
+        new_ranges = self.clip_intervals(shift=shift, width=width)
+
+        if weight is not None and not isinstance(weight, (int, float)):
+            raise TypeError("'width' must be an integer or float.")
+
+        cov, _ = create_np_interval_vector(new_ranges, force_size=width, value=weight)
+        return cov

+
+
+

+[docs]
+    def range(self) -> "IRanges":
+        """Concatenate all intervals. A tuple of minimum of all starts, maximum of all ends) in the object.
+
+        Args:
+            with_reverse_map (bool, optional): return map of indices back to
+                original object?. Defaults to False.
+
+        Returns:
+            IRanges: An new IRanges instance with a single range,
+            from the minimum start to the maximum end of the concatenated object.
+        """
+
+        min_start = min(self.start)
+        max_end = max(self.end)
+
+        return IRanges([min_start], [max_end - min_start])

+
+
+

+[docs]
+    def reduce(
+        self,
+        with_reverse_map: bool = False,
+        drop_empty_ranges: bool = False,
+        min_gap_width: int = 1,
+    ) -> "IRanges":
+        """`Reduce` orders the ranges, then merges overlapping or adjacent ranges.
+
+        Args:
+            with_reverse_map (bool, optional): Whether to return map of indices back to
+                original object. Defaults to False.
+            drop_empty_ranges (bool, optional): Whether to drop empty ranges. Defaults to False.
+            min_gap_width (int, optional): Ranges separated by a gap of at least ``min_gap_width``
+                positions are not merged. Defaults to 1.
+
+        Returns:
+            IRanges: A new ``IRanges`` object with reduced intervals.
+        """
+        if min_gap_width < 0:
+            raise ValueError("'min_gap_width' cannot be negative.")
+
+        _order = self.order()
+
+        result_starts = []
+        result_widths = []
+        result_revmaps = []
+        counter = 0
+
+        def get_elem_counter(idx):
+            elem = self[idx]
+            start = elem.start[0]
+            end = elem.end[0] - 1
+            width = elem.width[0]
+            return start, end, width
+
+        current_start, current_end, _ = get_elem_counter(_order[counter])
+        current_revmaps = [_order[counter]]
+
+        counter += 1
+        while counter < len(_order):
+            merge = False
+
+            o = _order[counter]
+            _idx_start, _idx_end, _idx_width = get_elem_counter(o)
+            _gap_width = _idx_start - current_end
+
+            if _gap_width <= min_gap_width:
+                merge = True
+
+            if merge is True:
+                if current_end < _idx_end:
+                    current_end = _idx_end
+
+                current_revmaps.append(o)
+                counter += 1
+            else:
+                if not (
+                    drop_empty_ranges is True and current_end - current_start + 1 == 0
+                ):
+                    result_starts.append(current_start)
+                    result_widths.append(current_end - current_start + 1)
+                    result_revmaps.append(current_revmaps)
+
+                current_revmaps = [o]
+                current_start = _idx_start
+                current_end = _idx_end
+                counter += 1
+
+        result_starts.append(current_start)
+        result_widths.append(current_end - current_start + 1)
+        result_revmaps.append(current_revmaps)
+
+        result = IRanges(result_starts, result_widths)
+
+        if with_reverse_map is True:
+            result.set_mcols(BiocFrame({"revmap": result_revmaps}), in_place=True)
+
+        return result

+
+
+    def _get_intervals_as_list(self) -> List[Tuple[int, int, int]]:
+        """Internal method to get intervals as a list of tuples.
+
+        Returns:
+            List[Tuple[int, int, int]]: List of tuples containing the start, end and the index.
+        """
+        intvals = []
+        for i in range(len(self)):
+            intvals.append((self.start[i], self.end[i], i))
+
+        return intvals
+
+

+[docs]
+    def order(self, decreasing: bool = False) -> List[int]:
+        """Get the order of indices for sorting.
+
+        Args:
+            decreasing (bool, optional): Whether to sort in descending order. Defaults to False.
+
+        Returns:
+            List[int]: List of integers indicating index position.
+        """
+        intvals = sorted(self._get_intervals_as_list(), reverse=decreasing)
+        order = [o[2] for o in intvals]
+        return order

+
+
+

+[docs]
+    def sort(self, decreasing: bool = False, in_place: bool = False) -> "IRanges":
+        """Sort the intervals.
+
+        Args:
+            decreasing (bool): Whether to sort in descending order. Defaults to False.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            sorted intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+        order = self.order(decreasing=decreasing)
+        output = self._define_output(in_place)
+        return output[order]

+
+
+

+[docs]
+    def gaps(self, start: Optional[int] = None, end: Optional[int] = None) -> "IRanges":
+        """Gaps returns an ``IRanges`` object representing the set of integers that remain after the intervals are
+        removed specified by the start and end arguments.
+
+        Args:
+            start (int, optional): Restrict start position. Defaults to 1.
+            end (int, optional): Restrict end position. Defaults to None.
+
+        Returns:
+            IRanges: A new ``IRanges`` is returned with the gaps.
+        """
+        _order = self.order()
+
+        overlap_start = min(self.start) if start is None else start
+        overlap_end = overlap_start - 1 if start is not None else None
+
+        result_starts = []
+        result_widths = []
+
+        def get_elem_counter(idx):
+            elem = self[idx]
+            start = elem.start[0]
+            end = elem.end[0] - 1
+            width = elem.width[0]
+            return start, end, width
+
+        for i in range(len(_order)):
+            _start, _end, _width = get_elem_counter(_order[i])
+
+            if _width == 0:
+                continue
+
+            if overlap_end is None:
+                overlap_end = _end
+            else:
+                _gap_start = overlap_end + 1
+
+                if end is not None and _start > end + 1:
+                    _start = end + 1
+
+                _gap_width = _start - _gap_start
+
+                if _gap_width >= 1:
+                    result_starts.append(_gap_start)
+                    result_widths.append(_gap_width)
+                    overlap_end = _end
+                elif _end > overlap_end:
+                    overlap_end = _end
+
+            if end is not None and overlap_end >= end:
+                break
+
+        if end is not None and overlap_end is not None and overlap_end < end:
+            result_starts.append(overlap_end + 1)
+            result_widths.append(end - overlap_end)
+
+        return IRanges(result_starts, result_widths)

+
+
+    # folows the same logic as in https://stackoverflow.com/questions/55480499/split-set-of-intervals-into-minimal-set-of-disjoint-intervals
+    # otherwise too much magic happening here - https://github.com/Bioconductor/IRanges/blob/5acb46b3f2805f7f74fe4cb746780e75f8257a83/R/inter-range-methods.R#L389
+

+[docs]
+    def disjoin(self, with_reverse_map: bool = False) -> "IRanges":
+        """Calculate disjoint intervals.
+
+        Args:
+            with_reverse_map (bool, optional): Whether to return a map of indices back to the original object.
+                Defaults to False.
+
+        Returns:
+            IRanges: A new `IRanges` containing disjoint intervals.
+        """
+        all_ints = []
+        counter = 0
+        for _, val in self:
+            all_ints.append((val.start[0], 1, counter))
+            all_ints.append((val.end[0], -1, counter))
+
+            counter += 1
+
+        sorted_ints = sorted(all_ints)
+
+        counter = 0
+        _current_start = None
+
+        result_starts = []
+        result_widths = []
+        result_revmaps = []
+
+        _curr_revmap = []
+        for x in sorted_ints:
+            _curr_revmap.append(x[2])
+
+            if _current_start is not None and x[0] > _current_start and counter != 0:
+                result_starts.append(_current_start)
+                result_widths.append(x[0] - _current_start)
+                result_revmaps.append(list(set(_curr_revmap)))
+                _curr_revmap = []
+
+            _current_start = x[0]
+            counter += x[1]
+
+        result = IRanges(result_starts, result_widths)
+
+        if with_reverse_map is True:
+            result.set_mcols(BiocFrame({"revmap": result_revmaps}), in_place=True)
+
+        return result

+
+
+    #############################
+    #### intra range methods ####
+    #############################
+
+

+[docs]
+    def shift(self, shift: int, in_place: bool = False) -> "IRanges":
+        """Shifts all the intervals by the amount specified by the ``shift`` argument.
+
+        Args:
+            shift (int): Amount to shift by.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            shifted intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+        if not isinstance(shift, int):
+            raise TypeError("'shift' must be an integer.")
+
+        output = self._define_output(in_place)
+        output._start = output._start + shift
+        return output

+
+
+    # TODO: not fully implemented
+

+[docs]
+    def narrow(
+        self,
+        start: Optional[int] = None,
+        width: Optional[int] = None,
+        end: Optional[int] = None,
+        in_place: bool = False,
+    ) -> "IRanges":
+        """Narrow genomic positions by provided ``start``, ``width`` and ``end`` parameters.
+
+        Important: These arguments are relative shift in positions for each range.
+
+        Args:
+            start (int, optional): Relative start position. Defaults to None.
+            width (int, optional): Relative end position. Defaults to None.
+            end (int, optional): Relative width of the interval. Defaults to None.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Raises:
+            ValueError: If `width` is provided, either `start` or `end` must be provided.
+            ValueError: Provide two of the three parameters - `start`, `end` and `width`
+                but not all.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            narrow intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+
+        if start is not None and end is not None and width is not None:
+            raise ValueError(
+                "Only provide two of the three parameters - 'start', "
+                "'end' and 'width' but not all!"
+            )
+
+        if width is not None:
+            if start is None and end is None:
+                raise ValueError(
+                    "If 'width' is provided, either 'start' or 'end' must be provided."
+                )
+
+        output = self._define_output(in_place)
+
+        all_starts = output.start.copy()
+        all_widths = output.width.copy()
+        all_ends = output.end.copy()
+
+        if start is not None:
+            if start > 0:
+                all_starts = all_starts + start - 1
+                all_widths = all_widths - start + 1
+            else:
+                all_starts = all_ends + start
+                all_widths = zeros(len(all_widths)) + start
+
+            if width is not None:
+                all_widths = zeros(len(all_widths)) + width
+            elif end is not None:
+                all_widths = all_widths + end + 1
+        elif end is not None:
+            if end < 0:
+                all_widths = all_widths + end - 1
+            else:
+                all_widths = zeros(len(all_widths)) + end
+
+            if width is not None:
+                all_widths = zeros(len(all_widths)) + width
+            elif end is not None:
+                all_widths = all_widths + end + 1
+
+        output._start = all_starts
+        output._width = all_widths
+        return output

+
+
+

+[docs]
+    def resize(
+        self,
+        width: int,
+        fix: Literal["start", "end", "center"] = "start",
+        in_place: bool = False,
+    ) -> "IRanges":
+        """Resize ranges to the specified ``width`` where either the ``start``, ``end``, or ``center`` is used as an
+        anchor.
+
+        Args:
+            width (int): Width to resize, must be non-negative!
+            fix (Literal["start", "end", "center"], optional): Fix positions by "start", "end", or "center".
+                Defaults to "start".
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Raises:
+            ValueError: If parameter ``fix`` is neither `start`, `end`, nor `center`.
+            ValueError: If ``width`` is negative.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            resized intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+
+        if width < 0:
+            raise ValueError("`width` cannot be negative!")
+
+        if fix not in ["start", "end", "center"]:
+            raise ValueError(
+                f"`fix` must be either 'start', 'end' or 'center', provided {fix}"
+            )
+
+        output = self._define_output(in_place)
+        if fix != "start":
+            if fix == "end":
+                output._start = output.start + output.width - width
+
+            if fix == "center":
+                output._start = output.start + output.width - (width / 2)
+
+        output._width = width
+        return output

+
+
+

+[docs]
+    def flank(
+        self, width: int, start: bool = True, both: bool = False, in_place: bool = False
+    ) -> "IRanges":
+        """Compute flanking ranges for each range. The logic is from the `IRanges` package.
+
+        If ``start`` is ``True`` for a given range, the flanking occurs at the `start`,
+        otherwise the `end`.
+        The `widths` of the flanks are given by the ``width`` parameter.
+
+        ``width`` can be negative, in which case the flanking region is
+        reversed so that it represents a prefix or suffix of the range.
+
+        Usage:
+
+            `ir.flank(3, True)`, where "x" indicates a range in ``ir`` and "-" indicates the
+            resulting flanking region:
+                ---xxxxxxx
+            If ``start`` were ``False``, the range in ``ir`` becomes
+                xxxxxxx---
+            For negative width, i.e. `ir.flank(x, -3, FALSE)`, where "*" indicates the overlap
+            between "x" and the result:
+                xxxx***
+            If ``both`` is ``True``, then, for all ranges in "x", the flanking regions are
+            extended into (or out of, if ``width`` is negative) the range, so that the result
+            straddles the given endpoint and has twice the width given by width.
+
+            This is illustrated below for `ir.flank(3, both=TRUE)`:
+                ---***xxxx
+
+        Args:
+            width (int): Width to flank by. May be negative.
+            start (bool, optional): Whether to only flank starts. Defaults to True.
+            both (bool, optional): Whether to flank both starts and ends. Defaults to False.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            flanked intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+
+        output = self._define_output(in_place)
+
+        if both is True:
+            width = abs(width)
+            if start is True:
+                output._start = output.start - width
+            else:
+                output._start = output.end - width
+
+            output._width = zeros(len(output)) + (2 * width)
+        else:
+            if start is True:
+                if width >= 0:
+                    output._start = output.start - width
+            else:
+                if width >= 0:
+                    output._start = output.end
+                else:
+                    output._start = output.end + width
+
+            output._width = zeros(len(output)) + abs(width)
+
+        return output

+
+
+

+[docs]
+    def promoters(
+        self, upstream: int = 2000, downstream: int = 200, in_place: bool = False
+    ) -> "IRanges":
+        """Extend intervals to promoter regions.
+
+        Generates promoter ranges relative to the transcription start site (TSS),
+        where TSS is start(x). The promoter range is expanded around the TSS
+        according to the upstream and downstream arguments. Upstream represents
+        the number of nucleotides in the 5' direction and downstream the number
+        in the 3' direction. The full range is defined as, (`start(x) - upstream`)
+        to (`start(x) + downstream - 1`).
+
+        Args:
+            upstream (int, optional): Number of positions to extend in the 5' direction.
+                Defaults to 2000.
+            downstream (int, optional): Number of positions to extend in the 3' direction.
+                Defaults to 200.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            promoter intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+
+        output = self._define_output(in_place)
+
+        if upstream < 0 or downstream < 0:
+            raise ValueError("'upstream' and 'downstream; must be integers >=0.")
+
+        new_starts = output.start - upstream
+        new_ends = output.start + downstream
+
+        output._start = new_starts
+        output._width = new_ends - new_starts
+        return output

+
+
+

+[docs]
+    def reflect(self, bounds: "IRanges", in_place: bool = False) -> "IRanges":
+        """Reverses each range in x relative to the corresponding range in bounds.
+
+        Reflection preserves the width of a range, but shifts it such the distance
+        from the left bound to the start of the range becomes the distance from the
+        end of the range to the right bound. This is illustrated below, where x
+        represents a range in x and [ and ] indicate the bounds:
+
+            [..xxx.....]
+            becomes
+            [.....xxx..]
+
+        Args:
+            bounds (IRanges): IRanges with the same length as the current object specifying the bounds.
+            in_place (bool): Whether to modify the object in place. Defaults to False.
+
+        Returns:
+            IRanges: If ``in_place = False``, a new ``IRanges`` is returned with the
+            reflected intervals. Otherwise, the current object is directly
+            modified and a reference to it is returned.
+        """
+
+        if not isinstance(bounds, IRanges):
+            raise TypeError("'bounds' must be an IRanges object.")
+
+        if len(bounds) != len(self):
+            raise ValueError("'bounds' does not contain the same number of intervals.")
+
+        output = self._define_output(in_place)
+        output._start = ((2 * bounds.start) + bounds.width) - output.end
+        return output

+
+
+

+[docs]
+    def restrict(
+        self,
+        start: Optional[int] = None,
+        end: Optional[int] = None,
+        keep_all_ranges: bool = False,
+    ) -> "IRanges":
+        """Restrict ranges to a given start and end positions.
+
+        Args:
+            start (int, optional): Start position. Defaults to None.
+            end (int, optional): End position. Defaults to None.
+            keep_all_ranges (bool, optional): Whether to keep intervals that do not overlap with start and end.
+                Defaults to False.
+
+        Returns:
+            IRanges: A new ``IRanges`` is returned with the
+            restricted intervals.
+        """
+        if start is None and end is None:
+            warn("Both 'start' and 'end' are 'None'.")
+            return self._define_output(False)
+
+        if start is not None:
+            new_starts = clip(self.start, start, None)
+        else:
+            new_starts = self.start
+
+        if end is not None:
+            new_ends = clip(self.end, None, end + 1)
+        else:
+            new_ends = self.end
+
+        new_starts = new_starts
+        new_widths = new_ends - new_starts
+
+        if keep_all_ranges is True:
+            new_widths = clip(new_widths, 0, None)
+        else:
+            _flt_idx = where(new_widths > -1)
+            new_starts = new_starts[_flt_idx]
+            new_widths = new_widths[_flt_idx]
+
+        return IRanges(new_starts, new_widths)

+
+
+

+[docs]
+    def overlap_indices(
+        self, start: Optional[int] = None, end: Optional[int] = None
+    ) -> List[int]:
+        """Find overlaps with the start and end positions.
+
+        Args:
+            start (int, optional): Start position. Defaults to None.
+            end (int, optional): End position. Defaults to None.
+
+        Returns:
+            List[int]: List of indices that overlap with the given range.
+        """
+        counter = 0
+        overlaps = []
+        for _, val in self:
+            keep_s = True
+            keep_e = True
+            _start = val.start[0]
+            _end = val.end[0] - 1
+
+            if start is not None and (_start < start):
+                keep_s = False
+
+            if end is not None and (_end > end):
+                keep_e = False
+
+            if keep_s is True or keep_e is True:
+                overlaps.append(counter)
+
+            counter += 1
+
+        return overlaps

+
+
+    ########################
+    #### set operations ####
+    ########################
+
+    # set operations
+

+[docs]
+    def union(self, other: "IRanges") -> "IRanges":
+        """Find union of intervals with `other`.
+
+        Args:
+            other (GenomicRanges): `IRanges` object.
+
+        Raises:
+            TypeError: If ``other`` is not `IRanges`.
+
+        Returns:
+            IRanges: A new `IRanges` object with all ranges.
+        """
+
+        if not isinstance(other, IRanges):
+            raise TypeError("'other' is not an IRanges object.")
+
+        all_starts = combine_seqs(self.start, other.start)
+        all_widths = combine_seqs(self.width, other.width)
+
+        output = IRanges(all_starts, all_widths)
+        output = output.reduce(min_gap_width=0, drop_empty_ranges=True)
+        return output

+
+
+

+[docs]
+    def setdiff(self, other: "IRanges") -> "IRanges":
+        """Find set difference with `other`.
+
+        Args:
+            other (GenomicRanges): `IRanges` object.
+
+        Raises:
+            TypeError: If ``other`` is not `IRanges`.
+
+        Returns:
+            IRanges: A new `IRanges` object.
+        """
+
+        if not isinstance(other, IRanges):
+            raise TypeError("'other' is not an IRanges object.")
+
+        all_starts = combine_seqs(self.start, other.start)
+        all_ends = combine_seqs(self.end, other.end)
+        start = min(all_starts)
+        end = max(all_ends)
+
+        x_gaps = self.gaps(start=start, end=end)
+        x_gaps_u = x_gaps.union(other)
+        diff = x_gaps_u.gaps(start=start, end=end)
+
+        return diff

+
+
+

+[docs]
+    def intersect(self, other: "IRanges") -> "IRanges":
+        """Find intersecting intervals with `other`.
+
+        Args:
+            other (GenomicRanges): `IRanges` object.
+
+        Raises:
+            TypeError: If ``other`` is not `IRanges`.
+
+        Returns:
+            IRanges: A new `IRanges` object with all intersecting intervals.
+        """
+
+        if not isinstance(other, IRanges):
+            raise TypeError("'other' is not an IRanges object.")
+
+        all_starts = combine_seqs(self.start, other.start)
+        all_ends = combine_seqs(self.end, other.end)
+        start = min(all_starts)
+        end = max(all_ends)
+
+        _gaps = other.gaps(start=start, end=end)
+        _inter = self.setdiff(_gaps)
+
+        return _inter

+
+
+    ############################
+    #### Overlap operations ####
+    ############################
+
+    def _build_ncls_index(self):
+        if not ut.package_utils.is_package_installed("ncls"):
+            raise ImportError("package: 'ncls' is not installed.")
+
+        from ncls import NCLS
+
+        if not hasattr(self, "_ncls"):
+            self._ncls = NCLS(
+                self.start, self.end, array([i for i in range(len(self))])
+            )
+
+    def _delete_ncls_index(self):
+        if hasattr(self, "_ncls"):
+            del self._ncls
+
+    def _generic_find_hits(
+        self,
+        query,
+        gap_start,
+        gap_end,
+        max_gap,
+        min_overlap,
+        select,
+        delete_index=False,
+    ):
+        self._build_ncls_index()
+
+        all_overlaps = []
+        for _, val in query:
+            _start = val.start[0]
+            _end = val.end[0]
+
+            _idx = []
+            new_start = _start - gap_start - 1
+            new_end = _end + gap_end + 1
+            _iter = self._ncls.find_overlap(new_start, new_end)
+
+            for i in _iter:
+                _gap, _overlap = calc_gap_and_overlap((_start, _end), (i[0], i[1]))
+                _append = True
+
+                if _gap is not None and _gap > max_gap:
+                    _append = False
+
+                if _overlap is not None and _overlap < min_overlap:
+                    _append = False
+
+                if _append is True:
+                    _idx.append(i[2])
+
+            if len(_idx) <= 1:
+                all_overlaps.append(_idx)
+            else:
+                if select == "first" or select == "arbitrary":
+                    all_overlaps.append([_idx[0]])
+                elif select == "last":
+                    all_overlaps.append([_idx[-1]])
+                elif select == "all":
+                    all_overlaps.append(_idx)
+
+        if delete_index is True:
+            self._delete_ncls_index()
+
+        return all_overlaps
+
+

+[docs]
+    def find_overlaps(
+        self,
+        query: "IRanges",
+        query_type: Literal["any", "start", "end", "within"] = "any",
+        select: Literal["all", "first", "last", "arbitrary"] = "all",
+        max_gap: int = -1,
+        min_overlap: int = 1,
+    ) -> List[List[int]]:
+        """Find overlaps with ``query`` `IRanges` object.
+
+        Args:
+            query (IRanges): Query `IRanges`.
+            query_type (Literal["any", "start", "end", "within"], optional): Overlap query type,
+                must be one of
+
+                - "any": Any overlap is good
+                - "start": Overlap at the beginning of the intervals
+                - "end": Must overlap at the end of the intervals
+                - "within": Fully contain the query interval
+
+                Defaults to "any".
+            select (Literal["all", "first", "last", "arbitrary"]): Determine what hit to choose when
+                there are multiple hits for an interval in ``subject``.
+            max_gap (int, optional): Maximum gap allowed in the overlap.
+                Defaults to -1 (no gap allowed).
+            min_overlap (int, optional): Minimum overlap with query. Defaults to 1.
+
+        Raises:
+            TypeError: If ``query`` is not an `IRanges` object.
+
+        Returns:
+            A List of indices that overlap with ``query``.
+        """
+
+        if not isinstance(query, IRanges):
+            raise TypeError("`query` is not a `IRanges` object.")
+
+        if query_type not in ["any", "start", "end", "within"]:
+            raise ValueError(
+                f"'query_type' must be one of {', '.join(['any', 'start', 'end', 'within'])}."
+            )
+
+        if select not in ["all", "first", "last", "arbitrary"]:
+            raise ValueError(
+                f"'select' must be one of {', '.join(['all', 'first', 'last', 'arbitrary'])}."
+            )
+
+        _tgap = 0 if max_gap == -1 else max_gap
+
+        all_overlaps = self._generic_find_hits(
+            query, _tgap, _tgap, max_gap, min_overlap, select, delete_index=True
+        )
+        return all_overlaps

+
+
+

+[docs]
+    def count_overlaps(
+        self,
+        query: "IRanges",
+        query_type: Literal["any", "start", "end", "within"] = "any",
+        max_gap: int = -1,
+        min_overlap: int = 1,
+    ) -> List[int]:
+        """Count number of overlaps with ``query`` `IRanges` object.
+
+        Args:
+            subject (IRanges): Query `IRanges`.
+            query_type (Literal["any", "start", "end", "within"], optional): Overlap query type,
+                must be one of
+
+                - "any": Any overlap is good
+                - "start": Overlap at the beginning of the intervals
+                - "end": Must overlap at the end of the intervals
+                - "within": Fully contain the query interval
+
+                Defaults to "any".
+            max_gap (int, optional): Maximum gap allowed in the overlap.
+                Defaults to -1 (no gap allowed).
+            min_overlap (int, optional): Minimum overlap with query. Defaults to 1.
+
+        Raises:
+            TypeError: If ``query`` is not an `IRanges` object.
+
+        Returns:
+            A List with number of overlaps.
+        """
+        _overlaps = self.find_overlaps(
+            query, query_type=query_type, max_gap=max_gap, min_overlap=min_overlap
+        )
+        return [len(x) for x in _overlaps]

+
+
+

+[docs]
+    def subset_by_overlaps(
+        self,
+        query: "IRanges",
+        query_type: Literal["any", "start", "end", "within"] = "any",
+        max_gap: int = -1,
+        min_overlap: int = 1,
+    ) -> "IRanges":
+        """Subset by overlap intervals in ``query`` `IRanges` object.
+
+        Args:
+            subject (IRanges): Query `IRanges`.
+            query_type (Literal["any", "start", "end", "within"], optional): Overlap query type,
+                must be one of
+
+                - "any": Any overlap is good
+                - "start": Overlap at the beginning of the intervals
+                - "end": Must overlap at the end of the intervals
+                - "within": Fully contain the query interval
+
+                Defaults to "any".
+            max_gap (int, optional): Maximum gap allowed in the overlap.
+                Defaults to -1 (no gap allowed).
+            min_overlap (int, optional): Minimum overlap with query. Defaults to 1.
+
+        Raises:
+            TypeError: If ``query`` is not of type `IRanges`.
+
+        Returns:
+            IRanges: A new `IRanges` object containing only subsets.
+        """
+        _overlaps = self.find_overlaps(
+            query=query, query_type=query_type, max_gap=max_gap, min_overlap=min_overlap
+        )
+        _all_indices = list(set(chain(*_overlaps)))
+        return self[_all_indices]

+
+
+    ###########################
+    #### search operations ####
+    ###########################
+
+    def _generic_search(
+        self, query, step_start, step_end, max_gap, min_overlap, select
+    ):
+        min_start = min(self.start)
+        max_end = max(self.end)
+        hits = []
+        for _, val in query:
+            _iterate = True
+            counter = 0
+            _hits = []
+
+            _tmin_overlap = min_overlap
+            if _tmin_overlap == -1:
+                _tmin_overlap = val.width[0] + 1
+
+            while _iterate is True:
+                all_overlaps = self._generic_find_hits(
+                    val,
+                    counter * step_start,
+                    counter * step_end,
+                    max_gap,
+                    _tmin_overlap,
+                    select,
+                    delete_index=False,
+                )
+
+                if len(all_overlaps[0]) > 0:
+                    _iterate = False
+                    _hits = all_overlaps[0]
+                    counter = 0
+                    break
+
+                counter += 1
+
+                if (
+                    (
+                        val.end[0] + (counter * step_end) + 1 > max_end + 1
+                        and val.start[0] - (counter * step_start) - 1 < min_start - 1
+                    )
+                    or (
+                        step_end == 0
+                        and val.start[0] - (counter * step_start) - 1 < min_start - 1
+                    )
+                    or (
+                        step_start == 0
+                        and val.end[0] + (counter * step_end) + 1 > max_end + 1
+                    )
+                ):
+                    _iterate = False
+                    _hits = []
+                    break
+
+            hits.append(_hits)
+
+        return hits
+
+

+[docs]
+    def nearest(
+        self, query: "IRanges", select: Literal["all", "arbitrary"] = "all"
+    ) -> List[List[int]]:
+        """Search nearest positions both upstream and downstream that overlap with each range in ``query``.
+
+        Args:
+            query (IRanges): Query `IRanges` to find nearest positions.
+            select (Literal["all", "arbitrary"]): Determine what hit to
+                choose when there are multiple hits for an interval in ``subject``.
+
+        Raises:
+            TypeError: If ``query`` is not of type `IRanges`.
+
+        Returns:
+            List[List[int]]: List of indices for each interval in query.
+        """
+
+        if not isinstance(query, IRanges):
+            raise TypeError("`query` is not a `IRanges` object.")
+
+        if select not in ["all", "arbitrary"]:
+            raise ValueError(
+                f"'select' must be one of {', '.join(['all', 'arbitrary'])}."
+            )
+
+        hits = self._generic_search(query, 1, 1, 10000000, 1, select)
+        self._delete_ncls_index()
+        return hits

+
+
+

+[docs]
+    def precede(
+        self, query: "IRanges", select: Literal["all", "first"] = "all"
+    ) -> List[List[int]]:
+        """Search nearest positions only downstream that overlap with each range in ``query``.
+
+        Args:
+            query (IRanges): Query `IRanges` to find nearest positions.
+            select (Literal["all", "first"]) Determine what hit to
+                choose when there are multiple hits for an interval in ``subject``.
+
+        Raises:
+            TypeError: If ``query`` is not of type `IRanges`.
+
+        Returns:
+            List[List[int]]: List of indices for each interval in query.
+        """
+
+        if not isinstance(query, IRanges):
+            raise TypeError("`query` is not a `IRanges` object.")
+
+        if select not in ["all", "first"]:
+            raise ValueError(f"'select' must be one of {', '.join(['all', 'first'])}.")
+
+        hits = self._generic_search(query, 0, 1, 10000000, -1, select)
+        self._delete_ncls_index()
+        return hits

+
+
+

+[docs]
+    def follow(
+        self, query: "IRanges", select: Literal["all", "last"] = "all"
+    ) -> List[List[int]]:
+        """Search nearest positions only downstream that overlap with each range in ``query``.
+
+        Args:
+            query (IRanges): Query `IRanges` to find nearest positions.
+            select (Literal["all", "last"]) Determine what hit to
+                choose when there are multiple hits for an interval in ``subject``.
+
+        Raises:
+            TypeError: If ``query`` is not of type `IRanges`.
+
+        Returns:
+            List[List[int]]: List of indices for each interval in query.
+        """
+
+        if not isinstance(query, IRanges):
+            raise TypeError("`query` is not a `IRanges` object.")
+
+        if select not in ["all", "last"]:
+            raise ValueError(f"'select' must be one of {', '.join(['all', 'last'])}.")
+
+        hits = self._generic_search(query, 1, 0, 10000000, -1, select)
+        self._delete_ncls_index()
+        return hits

+
+
+

+[docs]
+    def distance(self, query: "IRanges") -> List[int]:
+        """Calculate the pair-wise distance with intervals in query.
+
+        Args:
+            query (IRanges): Query `IRanges`.
+
+        Returns:
+            List[int]: A list containing distances.
+        """
+        if not isinstance(query, IRanges):
+            raise TypeError("`query` is not a `IRanges` object.")
+
+        if len(self) != len(query):
+            raise ValueError("'query' does not contain the same number of intervals.")
+
+        all_distances = []
+
+        for i in range(len(self)):
+            i_self = self[i]
+            i_query = query[i]
+            _gap, _overlap = calc_gap_and_overlap(
+                (i_self.start[0], i_self.end[0]), (i_query.start[0], i_query.end[0])
+            )
+
+            distance = _gap
+            if _gap is None:
+                distance = 0
+
+            all_distances.append(distance)
+
+        return all_distances

 

 
 
@@ -962,7 +2250,7 @@ 
Source code for iranges.IRanges
       
     
   

-

+

     
     
     
diff --git a/_modules/iranges/interval.html b/_modules/iranges/interval.html
new file mode 100644
index 0000000..465d6b3
--- /dev/null
+++ b/_modules/iranges/interval.html
@@ -0,0 +1,330 @@
+
+
+  
+    
+    
+
+    
+        iranges.interval - IRanges 0.1.0 documentation
+      
+    
+    
+    
+    
+
+
+
+  
+    
+    
+    
+
+
+  
+    Contents
+    
+      
+    
+  
+  
+    Menu
+    
+      
+      
+      
+    
+  
+  
+    Expand
+    
+      
+    
+  
+  
+    Light mode
+    
+      
+      
+      
+      
+      
+      
+      
+      
+      
+    
+  
+  
+    Dark mode
+    
+      
+      
+    
+  
+  
+    Auto light/dark mode
+    
+      
+      
+      
+      
+      
+      
+      
+    
+  
+
+
+
+
+
+
+
+
+
+

+  

+    

+      
+    

+    

+      
IRanges 0.1.0 documentation

+    

+    

+      

+        
+      

+      
+    

+  

+  
+  

+    

+      

+        
+          
+            
+          
+          Back to top
+        
+        

+          

+            
+          

+          
+        

+        

+          
Source code for iranges.interval
+from typing import List, Optional, Tuple, Union
+
+from numpy import ndarray, zeros
+
+__author__ = "jkanche"
+__copyright__ = "jkanche"
+__license__ = "MIT"
+
+
+

+[docs]
+def create_np_interval_vector(
+    intervals: "IRanges",
+    with_reverse_map: bool = False,
+    force_size: Optional[int] = None,
+    dont_sum: bool = False,
+    value: Union[int, float] = 1,
+) -> Tuple[ndarray, Optional[List]]:
+    """Represent intervals and calculate coverage.
+
+    Args:
+        intervals (IRanges): Input intervals.
+        with_reverse_map (bool, optional): Return map of indices? Defaults to False.
+        force_size (int, optional): Force size of the array.
+        dont_sum (bool, optional): Do not sum. Defaults to False.
+        value (Union[int, float], optional): Default value to increment. Defaults to 1.
+
+    Returns:
+        Tuple[ndarray, Optional[List]]: A numpy array representing
+        coverage from the intervals and optionally the index map.
+    """
+    if len(intervals) == 0:
+        return zeros(0), None
+
+    max_end = force_size
+    if max_end is None:
+        max_end = max(intervals.get_end())
+    else:
+        max_end += 1
+
+    cov = zeros(max_end)
+
+    revmap = None
+    if with_reverse_map:
+        revmap = [[] for _ in range(max_end)]
+
+    counter = 0
+    for name, row in intervals:
+        _start = row.start[0]
+        _end = row.end[0]
+
+        print(_start, _end)
+        if dont_sum:
+            cov[_start:_end] = value
+        else:
+            cov[_start:_end] += value
+
+        if with_reverse_map:
+            _ = [
+                revmap[x].append(name if name is not None else counter + 1)
+                for x in range(_start, _end)
+            ]
+
+        counter += 1
+    return cov[1:], revmap

+
+
+
+

+[docs]
+def calc_gap_and_overlap(
+    first: Tuple[int, int], second: Tuple[int, int]
+) -> Tuple[Optional[int], Optional[int]]:
+    """Calculate gap and/or overlap between two intervals.
+
+    Args:
+        first (Tuple): Interval containing start and end positions. `end` is non-inclusive.
+        second (Tuple): Interval containing start and end positions. `end` is non-inclusive.
+    """
+    _gap = None
+    _overlap = None
+
+    if first[0] < second[1] and first[1] > second[0]:
+        _overlap = min(first[1], second[1]) - max(first[0], second[0])
+    else:
+        _gap = None
+        if second[0] >= first[1]:
+            _gap = second[0] - first[1]
+        elif first[0] >= second[1]:
+            _gap = first[0] - second[1]
+
+    return (_gap, _overlap)

+
+

+        

+      

+      

+        
+        

+          
+          
+        

+        

+          

+            

+                Copyright © 2023, LTLA
+            

+            Made with Sphinx and @pradyunsg's
+            
+            Furo
+            
+          

+          

+            
+          

+        

+        
+      

+    

+    
+  

+

+    
+    
+    
+    
+
\ No newline at end of file
diff --git a/_sources/api/iranges.rst.txt b/_sources/api/iranges.rst.txt
index c7a74f2..6c7fa62 100644
--- a/_sources/api/iranges.rst.txt
+++ b/_sources/api/iranges.rst.txt
@@ -12,6 +12,14 @@ iranges.IRanges module
    :undoc-members:
    :show-inheritance:
 
+iranges.interval module
+-----------------------
+
+.. automodule:: iranges.interval
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 
diff --git a/_static/documentation_options.js b/_static/documentation_options.js
index d1f2291..13d90ff 100644
--- a/_static/documentation_options.js
+++ b/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.0.1',
+    VERSION: '0.1.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/api/iranges.html b/api/iranges.html
index 3099ba8..94627af 100644
--- a/api/iranges.html
+++ b/api/iranges.html
@@ -6,7 +6,7 @@
 
 
     
-        iranges package - IRanges 0.0.1 documentation
+        iranges package - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     

     

-      
IRanges 0.0.1 documentation

+      
IRanges 0.1.0 documentation

     

     

       

@@ -146,7 +146,7 @@
       

   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 

     
     
     
diff --git a/api/modules.html b/api/modules.html
index 36cd4e3..2ab8048 100644
--- a/api/modules.html
+++ b/api/modules.html
@@ -6,7 +6,7 @@
 
 
     
-        iranges - IRanges 0.0.1 documentation
+        iranges - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     

     

-      
IRanges 0.0.1 documentation

+      
IRanges 0.1.0 documentation

     

     

       

@@ -146,7 +146,7 @@
       

   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -209,28 +209,66 @@ 
iranges#<
 
  • IRanges.__copy__()
    • 
 
  • IRanges.__deepcopy__()
    • 
 
  • IRanges.__getitem__()
    • 
+
  • IRanges.__iter__()
    • 
 
  • IRanges.__len__()
    • 
 
  • IRanges.__repr__()
    • 
 
  • IRanges.__setitem__()
    • 
+
  • IRanges.clip_intervals()
    • 
+
  • IRanges.count_overlaps()
    • 
+
  • IRanges.coverage()
    • 
+
  • IRanges.disjoin()
    • 
+
  • IRanges.distance()
    • 
 
  • IRanges.end
    • 
+
  • IRanges.find_overlaps()
    • 
+
  • IRanges.flank()
    • 
+
  • IRanges.follow()
    • 
+
  • IRanges.gaps()
    • 
 
  • IRanges.get_end()
    • 
 
  • IRanges.get_mcols()
    • 
 
  • IRanges.get_metadata()
    • 
 
  • IRanges.get_names()
    • 
+
  • IRanges.get_row()
    • 
 
  • IRanges.get_start()
    • 
 
  • IRanges.get_width()
    • 
+
  • IRanges.intersect()
    • 
 
  • IRanges.mcols
    • 
 
  • IRanges.metadata
    • 
 
  • IRanges.names
    • 
+
  • IRanges.narrow()
    • 
+
  • IRanges.nearest()
    • 
+
  • IRanges.order()
    • 
+
  • IRanges.overlap_indices()
    • 
+
  • IRanges.precede()
    • 
+
  • IRanges.promoters()
    • 
+
  • IRanges.range()
    • 
+
  • IRanges.reduce()
    • 
+
  • IRanges.reflect()
    • 
+
  • IRanges.resize()
    • 
+
  • IRanges.restrict()
    • 
 
  • IRanges.set_mcols()
    • 
 
  • IRanges.set_metadata()
    • 
 
  • IRanges.set_names()
    • 
 
  • IRanges.set_start()
    • 
 
  • IRanges.set_width()
    • 
+
  • IRanges.setdiff()
    • 
+
  • IRanges.shift()
    • 
+
  • IRanges.sort()
    • 
 
  • IRanges.start
    • 
+
  • IRanges.subset_by_overlaps()
    • 
+
  • IRanges.union()
    • 
 
  • IRanges.width
    • 
 
 
+
  • IRangesIter
+
    • 
+
+
+
  • iranges.interval module
 
    • 
 
  • Module contents
    • 
@@ -289,7 +327,7 @@ 
    iranges#<
       
     
   
    
-
    
+
    
     
     
     
diff --git a/authors.html b/authors.html
index d6eedcf..d0c5139 100644
--- a/authors.html
+++ b/authors.html
@@ -6,7 +6,7 @@
 
 
     
-        Contributors - IRanges 0.0.1 documentation
+        Contributors - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -255,7 +255,7 @@ 
    Contributors
+
    
     
     
     
diff --git a/changelog.html b/changelog.html
index dc465b7..8649cae 100644
--- a/changelog.html
+++ b/changelog.html
@@ -6,7 +6,7 @@
 
 
     
-        Changelog - IRanges 0.0.1 documentation
+        Changelog - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -278,7 +278,7 @@ 
    Version 0.1 (development)
+
    
     
     
     
diff --git a/contributing.html b/contributing.html
index ed3419e..016c844 100644
--- a/contributing.html
+++ b/contributing.html
@@ -6,7 +6,7 @@
 
 
     
-        Contributing - IRanges 0.0.1 documentation
+        Contributing - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -519,7 +519,7 @@ 
    Releases
       
     
   
    
-
    
+
    
     
     
     
diff --git a/genindex.html b/genindex.html
index 1e6e0bc..ea0e5fb 100644
--- a/genindex.html
+++ b/genindex.html
@@ -4,7 +4,7 @@
     
     
 
-    Index - IRanges 0.0.1 documentation
+    Index - IRanges 0.1.0 documentation
 
     
     
@@ -121,7 +121,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -144,7 +144,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -198,7 +198,7 @@
           
 
    
   
    Index
    
-  
    _ | E | G | I | M | N | S | W
    
+  
    _ | C | D | E | F | G | I | M | N | O | P | R | S | U | W
    
 
    
 
    
   
    _
    
@@ -210,9 +210,17 @@ 
    _
    
 
         
  • __getitem__() (iranges.IRanges.IRanges method)
 
    • 
+        
  • __iter__() (iranges.IRanges.IRanges method)
+
+        
    • 
     
     
    
 
+
    
+  
    C
    
+  
+    
+    
+  
    
+
    
+
+
    
+  
    D
    
+  
+    
+    
+  
    
+
    
+
 
    
   
    E
    
   
@@ -232,10 +274,28 @@ 
    E
    
   
    
 
    
 
+
    
+  
    F
    
+  
+    
+    
+  
    
+
    
+
 
    
   
    G
    
   
-    
-    
+    
+  
    
     
     
    
+
    
+
+
    
+  
    U
    
+  
+    
    
   
    
@@ -377,7 +522,7 @@ 
    W
    
       
     
   
    
-
    
+
    
     
     
     
diff --git a/index.html b/index.html
index d671435..68c93e9 100644
--- a/index.html
+++ b/index.html
@@ -6,7 +6,7 @@
 
 
     
-        IRanges 0.0.1 documentation
+        IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -307,7 +307,7 @@ 
    Indices and tables
+
    
     
     
     
diff --git a/license.html b/license.html
index a24ee2d..a6cebcd 100644
--- a/license.html
+++ b/license.html
@@ -6,7 +6,7 @@
 
 
     
-        License - IRanges 0.0.1 documentation
+        License - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -274,7 +274,7 @@ 
    License#<
       
     
   
    
-
    
+
    
     
     
     
diff --git a/objects.inv b/objects.inv
index cc8b0a5..e6d7f74 100644
Binary files a/objects.inv and b/objects.inv differ
diff --git a/py-modindex.html b/py-modindex.html
index 439ff6a..cebc45c 100644
--- a/py-modindex.html
+++ b/py-modindex.html
@@ -4,7 +4,7 @@
     
     
 
-    Python Module Index - IRanges 0.0.1 documentation
+    Python Module Index - IRanges 0.1.0 documentation
 
     
     
@@ -121,7 +121,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -144,7 +144,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -214,6 +214,12 @@ 
    Python Module Index
    
         iranges
     
   
+  
+    
+       
+        iranges.interval
+    
+  
   
     
        
@@ -253,7 +259,7 @@ 
    Python Module Index
    
       
     
   
    
-
    
+
    
     
     
     
diff --git a/readme.html b/readme.html
index fb89b39..e21d37c 100644
--- a/readme.html
+++ b/readme.html
@@ -6,7 +6,7 @@
 
 
     
-        Integer ranges in Python - IRanges 0.0.1 documentation
+        Integer ranges in Python - IRanges 0.1.0 documentation
       
     
     
@@ -123,7 +123,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -146,7 +146,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -264,7 +264,7 @@ 
    Integer ranges in Python
+
    
     
     
     
diff --git a/search.html b/search.html
index ea87316..1a6f4ec 100644
--- a/search.html
+++ b/search.html
@@ -4,7 +4,7 @@
     
     
 
-    Search - IRanges 0.0.1 documentation
+    Search - IRanges 0.1.0 documentation
     
     
     
@@ -120,7 +120,7 @@
       
     
    
     
    
-      
    IRanges 0.0.1 documentation
    
+      
    IRanges 0.1.0 documentation
    
     
    
     
    
       
    
@@ -143,7 +143,7 @@
       
    
   
   
-  IRanges 0.0.1 documentation
+  IRanges 0.1.0 documentation
   
 
   
@@ -237,7 +237,7 @@
       
     
   
    
-
    
+
    
     
     
     
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index 167d749..1ed1135 100644
--- a/searchindex.js
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