[med-svn] [libseqlib] 01/01: Trying to adapt to patches of Debian fermi-lite
Andreas Tille
tille at debian.org
Thu Feb 2 17:42:39 UTC 2017
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tille pushed a commit to branch master
in repository libseqlib.
commit ec624861da9ad1f9a267b0a19068b971a9bcbd5a
Author: Andreas Tille <tille at debian.org>
Date: Thu Feb 2 18:41:52 2017 +0100
Trying to adapt to patches of Debian fermi-lite
---
debian/patches/adapt_to_debian_fermi-lite.patch | 169 ++++++++++++++++++++++++
debian/patches/fix_missing_declaration.patch | 11 ++
debian/patches/series | 4 +-
3 files changed, 183 insertions(+), 1 deletion(-)
diff --git a/debian/patches/adapt_to_debian_fermi-lite.patch b/debian/patches/adapt_to_debian_fermi-lite.patch
new file mode 100644
index 0000000..4d7a8ee
--- /dev/null
+++ b/debian/patches/adapt_to_debian_fermi-lite.patch
@@ -0,0 +1,169 @@
+Author: Andreas Tille <tille at 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
+@@ -129,7 +129,7 @@ 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 <bfc.h>
+
+ #include <stdexcept>
+ #include <algorithm>
+@@ -43,7 +44,7 @@ namespace SeqLib {
+ return false;
+
+ m_seqs_size = n;
+- m_seqs = (fseq1_t*)realloc(m_seqs, n * sizeof(fseq1_t));
++ m_seqs = (fml_seq1_t*)realloc(m_seqs, n * sizeof(fml_seq1_t));
+
+ if (!m_seqs)
+ return false;
+@@ -78,12 +79,12 @@ 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)
+@@ -96,7 +97,7 @@ namespace SeqLib {
+ if (!strlen(seq))
+ return false;
+
+- fseq1_t *s;
++ fml_seq1_t *s;
+
+ s = &m_seqs[n_seqs];
+
+@@ -245,12 +246,12 @@ namespace SeqLib {
+ void BFC::allocate_sequences_from_char(const std::vector<char*>& v) {
+
+ m_seqs_size = v.size();
+- m_seqs = (fseq1_t*)malloc(v.size() * sizeof(fseq1_t));
++ m_seqs = (fml_seq1_t*)malloc(v.size() * sizeof(fml_seq1_t));
+
+ 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[n_seqs];
+
+@@ -268,14 +269,14 @@ namespace SeqLib {
+
+ // alloc the memory
+ m_seqs_size = brv.size();
+- m_seqs = (fseq1_t*)malloc(brv.size() * sizeof(fseq1_t));
++ m_seqs = (fml_seq1_t*)malloc(brv.size() * sizeof(fml_seq1_t));
+
+ uint64_t size = 0;
+ for (BamRecordVector::const_iterator r = brv.begin(); r != brv.end(); ++r) {
+ // for (auto& r : brv) {
+ m_names.push_back(strdup(r->Qname().c_str()));
+
+- fseq1_t *s;
++ fml_seq1_t *s;
+
+ s = &m_seqs[n_seqs];
+
+--- 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];
+
+@@ -81,13 +81,13 @@ 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));
+
+ int m = 0;
+ 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];
+
+@@ -111,7 +111,7 @@ 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;
+@@ -164,7 +164,7 @@ 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));
diff --git a/debian/patches/fix_missing_declaration.patch b/debian/patches/fix_missing_declaration.patch
new file mode 100644
index 0000000..de6b94c
--- /dev/null
+++ b/debian/patches/fix_missing_declaration.patch
@@ -0,0 +1,11 @@
+--- a/src/BFC.cpp
++++ b/src/BFC.cpp
+@@ -348,7 +348,7 @@ namespace SeqLib {
+ // bfc_ch_t *ch; // set in BFC.h
+
+ // do the counting
+- ch = fml_count(n_seqs, m_seqs, bfc_opt.k, bfc_opt.q, bfc_opt.l_pre, bfc_opt.n_threads);
++ int ch = fml_count(n_seqs, m_seqs, bfc_opt.k, bfc_opt.q, bfc_opt.l_pre, bfc_opt.n_threads);
+
+ #ifdef DEBUG_BFC
+ // size of random hash value
diff --git a/debian/patches/series b/debian/patches/series
index 8c62d80..04f0f2c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,6 @@
use_debian_packaged_libs.patch
+adapt_to_debian_fermi-lite.patch
fix_fermi-lite_usage.patch
fix_htslib_usage.patch
-remove_duplicated_typedefs.patch
+# remove_duplicated_typedefs.patch
+# fix_missing_declaration.patch
--
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