From 9586c7a7cff5158028387056f6aff9a08773e127 Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Wed, 28 Aug 2024 06:15:23 -0500 Subject: [PATCH] be consistent with cigar position in the PAF --- src/common/wflign/src/wflign_patch.cpp | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/src/common/wflign/src/wflign_patch.cpp b/src/common/wflign/src/wflign_patch.cpp index eda9f95e..e7d45ae2 100644 --- a/src/common/wflign/src/wflign_patch.cpp +++ b/src/common/wflign/src/wflign_patch.cpp @@ -2269,17 +2269,15 @@ void write_alignment_paf( << "\t" << std::round(float2phred(1.0 - block_identity)) << "\t" //<< "as:i:" << aln.score << "\t" << "gi:f:" << gap_compressed_identity << "\t" - << "bi:f:" - << block_identity + << "bi:f:" << block_identity << "\t" + << "md:f:" << mashmap_estimated_identity << "\t" //<< "\t" << "ma:i:" << matches //<< "\t" << "mm:i:" << mismatches //<< "\t" << "ni:i:" << insertions //<< "\t" << "bi:i:" << inserted_bp //<< "\t" << "nd:i:" << deletions //<< "\t" << "bd:i:" << deleted_bp - << "\t" - << "cg:Z:" << cigar << "\t" - << "md:f:" << mashmap_estimated_identity; + << "cg:Z:" << cigar << "\t"; if (with_endline) { out << std::endl; }