From dec84c3ead1e663852ea79f8c5a4dde40d6b7c20 Mon Sep 17 00:00:00 2001
From: Florian Battke <Florian.Battke@cegat.de>
Date: Mon, 4 Jul 2022 14:30:42 +0200
Subject: [PATCH] Filter bad-cigar reads in bam streamer

These reads are ok according to SAM/BAM spec, but Manta can't work with them
---
 src/c++/lib/htsapi/bam_streamer.cpp | 36 ++++++++++++++++++++++++++++-
 src/c++/lib/htsapi/bam_streamer.hpp |  1 +
 2 files changed, 36 insertions(+), 1 deletion(-)

diff --git a/src/c++/lib/htsapi/bam_streamer.cpp b/src/c++/lib/htsapi/bam_streamer.cpp
index cddb2998..d61943cc 100644
--- a/src/c++/lib/htsapi/bam_streamer.cpp
+++ b/src/c++/lib/htsapi/bam_streamer.cpp
@@ -186,7 +186,7 @@ void bam_streamer::resetRegion(int referenceContigId, int beginPos, int endPos)
   _record_no     = 0;
 }
 
-bool bam_streamer::next()
+bool bam_streamer::next0()
 {
   if (nullptr == _hfp) return false;
 
@@ -223,6 +223,40 @@ bool bam_streamer::next()
   return _is_record_set;
 }
 
+bool bam_streamer::next() {
+  bool ret;
+  while ((ret=next0())) {
+    const auto cigar = _brec.raw_cigar();
+    if (_brec.n_cigar() > 1) {
+      int op0 = bam_cigar_op(cigar[0]);
+      int op1 = bam_cigar_op(cigar[1]);
+      int op_n0 = bam_cigar_op(cigar[_brec.n_cigar() - 1]);
+      int op_n1 = bam_cigar_op(cigar[_brec.n_cigar() - 2]);
+      if (
+        (op0 == BAM_CINS && op1 == BAM_CDEL) || //starts with ID
+        (op0 == BAM_CDEL && op1 == BAM_CINS) || //starts with DI
+        (op_n1 == BAM_CDEL && op_n0 == BAM_CINS) || //ends with DI
+        (op_n1 == BAM_CINS && op_n0 == BAM_CDEL) || //ends with ID
+        (op0 == BAM_CSOFT_CLIP && (op1==BAM_CDEL || op1==BAM_CINS)) ||  // starts with SD or SI 
+        ((op_n1 == BAM_CDEL || op_n1==BAM_CINS) && op_n0 == BAM_CSOFT_CLIP)  // ends with SD or SI
+      ) {
+        char op0cigar = (op0==BAM_CINS?'I':(op0==BAM_CDEL?'D':(op0==BAM_CSOFT_CLIP?'S':'x')));
+        char op1cigar = (op1==BAM_CINS?'I':(op1==BAM_CDEL?'D':(op1==BAM_CSOFT_CLIP?'S':'x')));
+        char opn1cigar = (op_n1==BAM_CINS?'I':(op_n1==BAM_CDEL?'D':(op_n1==BAM_CSOFT_CLIP?'S':'x')));
+        char opn0cigar = (op_n0==BAM_CINS?'I':(op_n0==BAM_CDEL?'D':(op_n0==BAM_CSOFT_CLIP?'S':'x')));
+        std::cout << "Skipping read: " << _brec.qname() << " CIGAR edges: " 
+           << " " << op0cigar << op1cigar <<"..."<< opn1cigar<<opn0cigar <<"\n";
+        // unusable read, made by abra realigner, load next
+      } else {
+        break;  // cigar seems ok
+      }
+    } else {
+      break;   // single-item cigar is always ok
+    }
+  }
+  return ret;
+}
+
 const char* bam_streamer::target_id_to_name(const int32_t tid) const
 {
   // assert(tid < _bfp->header->n_targets);
diff --git a/src/c++/lib/htsapi/bam_streamer.hpp b/src/c++/lib/htsapi/bam_streamer.hpp
index f181e202..81f68369 100644
--- a/src/c++/lib/htsapi/bam_streamer.hpp
+++ b/src/c++/lib/htsapi/bam_streamer.hpp
@@ -76,6 +76,7 @@ struct bam_streamer : public stream_state_reporter, public boost::noncopyable {
   void resetRegion(int referenceContigId, int beginPos, int endPos);
 
   bool next();
+  bool next0();
 
   const bam_record* get_record_ptr() const
   {