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cpp/src/bam/BamReader.cpp

@@ -1,6 +1,6 @@
 /***************************************************************************************************
  *
- * Copyright (C) 2025 Genome4me Incorporated - All Rights Reserved.
+ * Copyright (C) 2025-2026 Genome4me Incorporated - All Rights Reserved.
  *
  * This software, including its source code, embedded concepts, and associated
  * documentation, is proprietary to Genome4me Incorporated and is protected
@@ -22,10 +22,10 @@
 #include <utility>
 
 namespace deeprm {
-  BamReader::BamReader(const string& path, int bq_threshold, char boi,
+  BamReader::BamReader(const string& path, int bq_threshold, char boi, int filter_flag,
                        unordered_map<string, int>& ref_index_dict)
     : bam_path(path), bq_cutoff(bq_threshold), base_of_interest(boi),
-      ref_index_dict(ref_index_dict)
+      filter_flag(filter_flag), ref_index_dict(ref_index_dict)
   {
   }
 
@@ -370,8 +370,21 @@ namespace deeprm {
 
   void BamReader::process_read(bam1_t* read, vector<BamRecord>& records)
   {
+    // BAM_FUNMAP and l_qseq==0 are unconditional safety checks: downstream
+    // code dereferences reference and sequence, so an unmapped record (tid
+    // == -1, no CIGAR) or a sequence-less secondary alignment (the BAM
+    // standard stores secondaries with seq='*', i.e. l_qseq==0) would
+    // crash. The default `-g 276` happens to mask both via its 4 (UNMAP)
+    // and 256 (SECONDARY) bits, but any user-supplied -g value missing
+    // them — e.g. `-g 0`, `-g 4`, `-g 16` — would let the unsafe records
+    // through. These two checks make the path safe for any -g value.
+    //
+    // filter_flag is then the user-tunable SAM-flag mask, kept identical to
+    // MergedDataWorker's no-C path so that -C and no-C produce the same
+    // record set for any -g value.
     if (read->core.flag & BAM_FUNMAP) return;
     if (read->core.l_qseq == 0) return;
+    if (read->core.flag & filter_flag) return;
 
     // Check for mv tag
     uint8_t* mv_tag = bam_aux_get(read, "mv");

cpp/src/bam/BamReader.h

@@ -1,6 +1,6 @@
 /***************************************************************************************************
  *
- * Copyright (C) 2025 Genome4me Incorporated - All Rights Reserved.
+ * Copyright (C) 2025-2026 Genome4me Incorporated - All Rights Reserved.
  *
  * This software, including its source code, embedded concepts, and associated
  * documentation, is proprietary to Genome4me Incorporated and is protected
@@ -44,6 +44,7 @@ namespace deeprm {
     string bam_path;
     int bq_cutoff;
     char base_of_interest;
+    int filter_flag;  // SAM flag bits to exclude (matches MergedDataWorker no-C path)
     unordered_map<string, int> ref_index_dict;
 
     vector<pair<int32_t, int32_t>> get_aligned_pairs(bam1_t* read, char boi);
@@ -52,7 +53,7 @@ namespace deeprm {
     uint32_t get_md_reference_length(const char* md_tag);
 
   public:
-    BamReader(const string& path, int bq_threshold, char boi,
+    BamReader(const string& path, int bq_threshold, char boi, int filter_flag,
               unordered_map<string, int>& ref_index_dict);
     ~BamReader();
 

cpp/src/main.cpp

@@ -97,7 +97,8 @@ void process_bam_worker(int worker_id, int num_workers, const Arguments& args,
 {
   log_info() << "Starting BAM worker " << worker_id << endl;
 
-  BamReader reader(args.bam_path, args.qcut, args.base_of_interest, ref_index_dict);
+  BamReader reader(args.bam_path, args.qcut, args.base_of_interest,
+                   args.filter_flag, ref_index_dict);
   auto records = reader.parse_bam(worker_id, num_workers, args.bam_threads);
 
   size_t record_count = records.size(); // Save size before move

cpp/src/merger/MergedDataWorker.cpp

@@ -1,6 +1,6 @@
 /***************************************************************************************************
  *
- * Copyright (C) 2025 Genome4me Incorporated - All Rights Reserved.
+ * Copyright (C) 2025-2026 Genome4me Incorporated - All Rights Reserved.
  *
  * This software, including its source code, embedded concepts, and associated
  * documentation, is proprietary to Genome4me Incorporated and is protected
@@ -222,6 +222,18 @@ namespace deeprm {
   bool MergedDataWorker::convert_bam1_to_record(bam1_t* read, sam_hdr_t* header,
                                                 BamRecord& record) const
   {
+    // BAM_FUNMAP and l_qseq==0 are unconditional safety checks: downstream
+    // code dereferences reference and sequence, so an unmapped record (tid
+    // == -1, no CIGAR) or a sequence-less secondary alignment (the BAM
+    // standard stores secondaries with seq='*', i.e. l_qseq==0) would
+    // crash. The default `-g 276` happens to mask both via its 4 (UNMAP)
+    // and 256 (SECONDARY) bits, but any user-supplied -g value missing
+    // them — e.g. `-g 0`, `-g 4`, `-g 16` — would let the unsafe records
+    // through. These two checks make the path safe for any -g value.
+    if (read->core.flag & BAM_FUNMAP)
+      return false;
+    if (read->core.l_qseq == 0)
+      return false;
     if (read->core.flag & args.filter_flag)
       return false;