Use bam_cigar2qlen for query length calculation#1388
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Summary
calculateQueryLengthWithoutHardClippingwith a call to HTSlib'sbam_cigar2qlen()calculateQueryLengthWithHardClippingto callbam_cigar2qlen()and then scan only forBAM_CHARD_CLIPoperations (typically 0-2 at CIGAR ends)Test plan
REF_PATH=: pytest tests/AlignedSegment_test.py -vAI disclosure: This PR was AI-assisted using Claude Code. The issue was identified via AI-guided code review, and the implementation was drafted by AI with human review and approval.