patched GSamReader::next() memory leak

gpertea · gpertea · commit 9d9614927b0d · 2021-11-03T16:24:29.000-04:00
diff --git a/gclib/GSam.h b/gclib/GSam.h
@@ -140,7 +140,117 @@ class GSamRecord: public GSeg {
     ~GSamRecord() {
        clear();
     }
+/*
+    void print_cigar(bam1_t *al){
+        for (uint8_t c=0;c<al->core.n_cigar;++c){
+            uint32_t *cigar_full=bam_get_cigar(al);
+            int opcode=bam_cigar_op(cigar_full[c]);
+            int length=bam_cigar_oplen(cigar_full[c]);
+            std::cout<<length<<bam_cigar_opchr(opcode);
+        }
+        std::cout<<std::endl;
+    }
+
+    void print_seq(bam1_t *new_rec){
+        int32_t qlen = new_rec->core.l_qseq;
+        int8_t *buf = NULL;
+        buf = static_cast<int8_t *>(realloc(buf, qlen+1));
+        buf[qlen] = '\0';
+        uint8_t* seq = bam_get_seq(new_rec);
+        for (int i = 0; i < qlen; ++i)
+            buf[i] = bam_seqi(seq, i);
+        for (int i = 0; i < qlen; ++i) {
+            buf[i] = seq_nt16_str[buf[i]];
+        }
+        std::string str_seq((char*)(char*)buf);
+        std::cout<<str_seq<<std::endl;
+    }
+*/
+    // taken from samtools/bam_import.c
+    static inline uint8_t * alloc_data(bam1_t *b, size_t size)
+    {
+        if (b->m_data < size)
+        {
+            b->m_data = size;
+            kroundup32(b->m_data);
+            b->data = (uint8_t*)realloc(b->data, b->m_data);
+        }
+        return b->data;
+    }
+
+    bam1_t * bam_update(bam1_t * b,
+                        const size_t nbytes_old,
+                        const size_t nbytes_new,
+                        uint8_t * field_start){ // from pysam
+        int d = nbytes_new - nbytes_old;
+        int new_size;
+        size_t nbytes_before;
+        uint8_t * retval = NULL;
+
+        // no change
+        if (d == 0)
+            return b;
+
+        // new size of total data
+        new_size = d + b->l_data;
+
+        // fields before field in data
+        nbytes_before = field_start - b->data;
+/*
+        if (b->l_data != 0)
+        {
+            assert(nbytes_before >= 0);
+            assert(nbytes_before <= b->l_data);
+        }
+*/
+        // increase memory if required
+        if (d > 0)
+        {
+            retval = alloc_data(b, new_size);
+            if (retval == NULL)
+                return NULL;
+            field_start = b->data + nbytes_before;
+        }
+
+        // move data after field to new location
+        memmove(field_start + nbytes_new,
+                field_start + nbytes_old,
+                b->l_data - (nbytes_before + nbytes_old));
 
+        // adjust l_data
+        b->l_data = new_size;
+
+        return b;
+    }
+/*
+    void replace_qname(int id){ // replace the name with an ID
+        char * p = bam_get_qname(b);
+
+        std::string qname = std::to_string(id);
+        int l = qname.size()+1;
+        int l_extranul = 0;
+        if (l % 4 != 0){
+            l_extranul = 4 - l % 4;
+        }
+
+        bam1_t * retval = bam_update(b,b->core.l_qname,l + l_extranul,(uint8_t*)p);
+        if (retval == NULL){
+            GError("Could not allocate memory");
+        }
+
+        b->core.l_extranul = l_extranul;
+        b->core.l_qname = l + l_extranul;
+
+        p = bam_get_qname(b);
+
+        strcpy(p,qname.c_str());
+        uint16_t x = 0;
+
+        for (int x=l;x<l+l_extranul;x++){
+            p[x] = '\0';
+        }
+    }
+*/
     void parse_error(const char* s) {
       GError("SAM parsing error: %s\n", s);
     }
@@ -381,6 +491,7 @@ class GSamReader {
         GSamRecord* bamrec=new GSamRecord(b, hdr, true);
         return bamrec;
       }
+      bam_destroy1(b);
       return NULL;
    }
 
