From 492af26026285ac86fa873ad00e59643cf45efe7 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Mon, 24 Jun 2024 09:40:24 +0200
Subject: [PATCH 1/2] do not add suffixes to the query names when it is split
 in SAM format

---
 src/align/include/computeAlignments.hpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/align/include/computeAlignments.hpp b/src/align/include/computeAlignments.hpp
index 2cb11a65..51bed386 100644
--- a/src/align/include/computeAlignments.hpp
+++ b/src/align/include/computeAlignments.hpp
@@ -482,7 +482,7 @@ typedef atomic_queue::AtomicQueue<std::string*, 1024, nullptr, true, true, false
           }
 
           // To distinguish split alignment in SAM output format (currentRecord.rankMapping == 0 to avoid the suffix there is just one alignment for the query)
-          const std::string query_name_suffix = param.split && param.sam_format ? "_" + std::to_string(rec->currentRecord.rankMapping) : "";
+          //const std::string query_name_suffix = param.split && param.sam_format ? "_" + std::to_string(rec->currentRecord.rankMapping) : "";
 
           wflign::wavefront::WFlign* wflign = new wflign::wavefront::WFlign(
               param.wflambda_segment_length,
@@ -523,7 +523,7 @@ typedef atomic_queue::AtomicQueue<std::string*, 1024, nullptr, true, true, false
               !param.sam_format,
               param.no_seq_in_sam);
           wflign->wflign_affine_wavefront(
-              rec->currentRecord.qId + query_name_suffix,
+              rec->currentRecord.qId,// + query_name_suffix,
               queryRegionStrand,
               rec->queryTotalLength,
               rec->queryStartPos,

From 7ccbb40ff1272df8ab79b95251d0f4114feddb21 Mon Sep 17 00:00:00 2001
From: AndreaGuarracino <andreaguarracino@outlook.com>
Date: Mon, 24 Jun 2024 10:34:54 +0200
Subject: [PATCH 2/2] manage HARD clipping properly

---
 src/common/wflign/src/wflign_patch.cpp | 20 ++++----------------
 1 file changed, 4 insertions(+), 16 deletions(-)

diff --git a/src/common/wflign/src/wflign_patch.cpp b/src/common/wflign/src/wflign_patch.cpp
index 0754856f..25544fe0 100644
--- a/src/common/wflign/src/wflign_patch.cpp
+++ b/src/common/wflign/src/wflign_patch.cpp
@@ -1715,24 +1715,12 @@ query_start : query_end)
                     query_offset +
                     (query_is_rev ? query_length - query_start : query_end);
 
-            if (query_is_rev) {
-                if (query_length > query_end_pos) {
-                    out << (query_length - query_end_pos) << "H";
-                }
-            } else {
-                if (query_start_pos > 0) {
-                    out << query_start_pos << "H";
-                }
+            if (query_start_pos > 0) {
+                out << query_start_pos << "H";
             }
             out << cigarv;
-            if (query_is_rev) {
-                if (query_start_pos > 0) {
-                    out << query_start_pos << "H";
-                }
-            } else {
-                if (query_length > query_end_pos) {
-                    out << (query_length - query_end_pos) << "H";
-                }
+            if (query_total_length > query_end_pos) {
+                out << (query_total_length - query_end_pos) << "H";
             }
 
             out << "\t"