Merge pull request #253 from waveygang/polite_sam_format

Fix SAM format output and HARD clipping
waveygang · Jul 1, 2024 · a8e012f · a8e012f
2 parents 44d2ba0 + 7ccbb40
commit a8e012f
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Showing 2 changed files with 6 additions and 18 deletions.
diff --git 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,

diff --git 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"