From 9a694d04fd0cb0dee3265fddb0376951dd811f8e Mon Sep 17 00:00:00 2001
From: Marcel Martin <marcel.martin@scilifelab.se>
Date: Tue, 13 Feb 2024 21:59:20 +0100
Subject: [PATCH] Add AlignedSegment.__repr__ displaying the most useful fields
 (PR #1267)

Example output:
<AlignedSegment('name', flags=16=0x10, ref='chr1', zpos=1170070, mapq=255, cigar='50M', ...)>

[Use an f-string; write flags in hex too; and use 'zpos' label to emphasis
this field is shown 0-based. -- JM]
---
 pysam/libcalignedsegment.pyx | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pysam/libcalignedsegment.pyx b/pysam/libcalignedsegment.pyx
index d688eacd..3bf73a6c 100644
--- a/pysam/libcalignedsegment.pyx
+++ b/pysam/libcalignedsegment.pyx
@@ -978,6 +978,9 @@ cdef class AlignedSegment:
                                    self.query_qualities,
                                    self.tags)))
 
+    def __repr__(self):
+        return f'<{type(self).__name__}({self.query_name!r}, flags={self.flag}={self.flag:#x}, ref={self.reference_name!r}, zpos={self.reference_start}, mapq={self.mapping_quality}, cigar={self.cigarstring!r}, ...)>'
+
     def __copy__(self):
         return makeAlignedSegment(self._delegate, self.header)