Describe pysam's equivalents to `samtools idxstats` statistics
Document that get_index_statistics returns the contig statistics
from `samtools idxstats` while nocoordinate corresponds to the "*"
statistics printed for unplaced unmapped reads. Addresses
@@ -1779,7 +1779,8 @@ cdef class AlignmentFile(HTSFile):
property nocoordinate:
"""int with total number of reads without coordinates according to the
- statistics recorded in the index. This is a read-only attribute.
+ statistics recorded in the index, i.e., the statistic printed for "*"
+ by the ``samtools idxstats`` command. This is a read-only attribute.
"""
def __get__(self):
self.check_index()
@@ -1790,7 +1791,8 @@ cdef class AlignmentFile(HTSFile):
def get_index_statistics(self):
"""return statistics about mapped/unmapped reads per chromosome as
- they are stored in the index.
+ they are stored in the index, similarly to the statistics printed
+ by the ``samtools idxstats`` command.
Returns:
list :
