Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
Description: In Debian's fermi-lite 0.1-3 a name space pollution with
 bwa was resolved.  This solution was different to the one libseqlib
 author was doing in his private copy of fermi-lite

--- a/SeqLib/BFC.h
+++ b/SeqLib/BFC.h
@@ -117,7 +117,7 @@ namespace SeqLib {
     float kcov;
 
     // reads to correct in place
-    fseq1_t * m_seqs;
+    fml_seq1_t * m_seqs;
 
     // number of sequeces
     size_t n_seqs;
--- a/SeqLib/FermiAssembler.h
+++ b/SeqLib/FermiAssembler.h
@@ -117,7 +117,7 @@ namespace SeqLib {
   private:
 
     // reads to assemble
-    fseq1_t *m_seqs;
+    fml_seq1_t *m_seqs;
   
     // size of m_seqs
     size_t m;
--- a/src/BFC.cpp
+++ b/src/BFC.cpp
@@ -31,6 +31,7 @@ SOFTWARE.
 */
 
 #include "SeqLib/BFC.h"
+#include <fml/bfc.h>
 
 #include <stdexcept>
 #include <algorithm>
@@ -42,12 +43,12 @@ namespace SeqLib {
     // do the intial allocation
     if (n_seqs == 0 && !m_seqs) {
       m_seqs_size = 32;
-      m_seqs = (fseq1_t*)malloc(m_seqs_size * sizeof(fseq1_t));
+      m_seqs = (fml_seq1_t*)malloc(m_seqs_size * sizeof(fml_seq1_t));
     }
     // realloc if not enough space
     else if (n_seqs >= m_seqs_size) {
       m_seqs_size = 2 * m_seqs_size;
-      m_seqs = (fseq1_t*)realloc(m_seqs, m_seqs_size * sizeof(fseq1_t));
+      m_seqs = (fml_seq1_t*)realloc(m_seqs, m_seqs_size * sizeof(fml_seq1_t));
     }
 
     if (!m_seqs)
@@ -60,7 +61,7 @@ namespace SeqLib {
     if (!strlen(seq))
       return false;
 
-    fseq1_t *s;
+    fml_seq1_t *s;
     
     s = &m_seqs[n_seqs];
     
@@ -108,13 +109,13 @@ namespace SeqLib {
     assert(n_seqs == 0);
     assert(m_names.size() == 0);
 
-    m_seqs = (fseq1_t*)malloc(1 * sizeof(fseq1_t));
+    m_seqs = (fml_seq1_t*)malloc(1 * sizeof(fml_seq1_t));
     n_seqs = 1;
     
     //uint64_t size = 0;
     //for (std::vector<char*>::const_iterator r = v.begin(); r != v.end(); ++r) {
     //    for (auto& r : v) {
-    fseq1_t *s;
+    fml_seq1_t *s;
     s = &m_seqs[0];
     s->seq   = strdup(str.c_str());
     s->qual  = q.empty() || q.length() != str.length() ? NULL : strdup(q.c_str()); 
--- a/src/FermiAssembler.cpp
+++ b/src/FermiAssembler.cpp
@@ -41,13 +41,13 @@ namespace SeqLib {
     // dynamically alloc the memory
     if (m <= n_seqs)
       m = m <= 0 ? 32 : (m*2); // if out of mem, double it
-    m_seqs = (fseq1_t*)realloc(m_seqs, m * sizeof(fseq1_t));
+    m_seqs = (fml_seq1_t*)realloc(m_seqs, m * sizeof(fml_seq1_t));
     
     // add the name
     m_names.push_back(r.Name);
 
     // construct the seq
-    fseq1_t *s;
+    fml_seq1_t *s;
     s = &m_seqs[n_seqs];
     s->seq   = strdup(r.Seq.c_str());
     s->qual = r.Qual.empty() ? NULL : strdup(r.Qual.c_str());
@@ -61,11 +61,11 @@ namespace SeqLib {
 
     // alloc the memory
     m = n_seqs + v.size();
-    m_seqs = (fseq1_t*)realloc(m_seqs, m * sizeof(fseq1_t));
+    m_seqs = (fml_seq1_t*)realloc(m_seqs, m * sizeof(fml_seq1_t));
 
     for (UnalignedSequenceVector::const_iterator r = v.begin(); r != v.end(); ++r) {
       m_names.push_back(r->Name);
-      fseq1_t *s;
+      fml_seq1_t *s;
 
       s = &m_seqs[n_seqs];
 
@@ -81,12 +81,12 @@ namespace SeqLib {
   void FermiAssembler::AddReads(const BamRecordVector& brv) {
 
     // alloc the memory
-    m_seqs = (fseq1_t*)realloc(m_seqs, (n_seqs + brv.size()) * sizeof(fseq1_t));
+    m_seqs = (fml_seq1_t*)realloc(m_seqs, (n_seqs + brv.size()) * sizeof(fml_seq1_t));
 
     uint64_t size = 0;
     for (BamRecordVector::const_iterator r = brv.begin(); r != brv.end(); ++r) {
       m_names.push_back(r->Qname());
-      fseq1_t *s;
+      fml_seq1_t *s;
       
       s = &m_seqs[n_seqs];
       
@@ -110,7 +110,7 @@ namespace SeqLib {
       return; //already cleared
 
     for (size_t i = 0; i < n_seqs; ++i) {
-      fseq1_t * s = &m_seqs[i];
+      fml_seq1_t * s = &m_seqs[i];
       if (s->qual)
        free(s->qual); 
       s->qual = NULL;
@@ -163,7 +163,7 @@ namespace SeqLib {
     
     UnalignedSequenceVector r;
     for (size_t i = 0; i < n_seqs; ++i) {
-      fseq1_t * s = &m_seqs[i];
+      fml_seq1_t * s = &m_seqs[i];
       UnalignedSequence read;
       if (s->seq)
 	read.Seq = (std::string(s->seq));