No longer refer to deprecated attributes
@@ -1362,8 +1362,8 @@ cdef class AlignedSegment:
The length includes soft-clipped bases and is equal to
``len(query_sequence)``.
- This property is read-only but can be set by providing a
- sequence.
+ This property is read-only but is updated when a new query
+ sequence is assigned to this AlignedSegment.
Returns 0 if not available.
@@ -1382,7 +1382,7 @@ cdef class AlignedSegment:
"""read sequence bases, including :term:`soft clipped` bases
(None if not present).
- Note that assigning to seq will invalidate any quality scores.
+ Assigning to this attribute will invalidate any quality scores.
Thus, to in-place edit the sequence and quality scores, copies of
the quality scores need to be taken. Consider trimming for example::
@@ -1645,7 +1645,7 @@ cdef class AlignedSegment:
property reference_length:
'''aligned length of the read on the reference genome.
- This is equal to `aend - pos`. Returns None if not available.'''
+ This is equal to `reference_end - reference_start`. Returns None if not available.'''
def __get__(self):
cdef bam1_t * src
src = self._delegate
@@ -1657,9 +1657,9 @@ cdef class AlignedSegment:
property query_alignment_sequence:
"""aligned portion of the read.
- This is a substring of :attr:`seq` that excludes flanking
+ This is a substring of :attr:`query_sequence` that excludes flanking
bases that were :term:`soft clipped` (None if not present). It
- is equal to ``seq[qstart:qend]``.
+ is equal to ``query_sequence[query_alignment_start:query_alignment_end]``.
SAM/BAM files may include extra flanking bases that are not
part of the alignment. These bases may be the result of the
@@ -1692,9 +1692,9 @@ cdef class AlignedSegment:
property query_alignment_qualities:
"""aligned query sequence quality values (None if not present). These
- are the quality values that correspond to :attr:`query`, that
+ are the quality values that correspond to :attr:`query_alignment_sequence`, that
is, they exclude qualities of :term:`soft clipped` bases. This
- is equal to ``qual[qstart:qend]``.
+ is equal to ``query_qualities[query_alignment_start:query_alignment_end]``.
Quality scores are returned as a python array of unsigned
chars. Note that this is not the ASCII-encoded value typically
@@ -1727,7 +1727,7 @@ cdef class AlignedSegment:
"""start index of the aligned query portion of the sequence (0-based,
inclusive).
- This the index of the first base in :attr:`seq` that is not
+ This the index of the first base in :attr:`query_sequence` that is not
soft-clipped.
"""
def __get__(self):
@@ -1737,7 +1737,7 @@ cdef class AlignedSegment:
"""end index of the aligned query portion of the sequence (0-based,
exclusive)
- This the index just past the last base in :attr:`seq` that is not
+ This the index just past the last base in :attr:`query_sequence` that is not
soft-clipped.
"""
def __get__(self):
@@ -1746,7 +1746,7 @@ cdef class AlignedSegment:
property query_alignment_length:
"""length of the aligned query sequence.
- This is equal to :attr:`qend` - :attr:`qstart`"""
+ This is equal to :attr:`query_alignment_end` - :attr:`query_alignment_start`"""
def __get__(self):
cdef bam1_t * src
src = self._delegate
