[med-svn] [libseqlib] 01/01: Further adaptions to get rid of fermi-lite fork

[Andreas Tille]

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tille pushed a commit to branch master
in repository libseqlib.

commit c8c6868c2324a6a405278d31d31cd6fc7334256e
Author: Andreas Tille <tille at debian.org>
Date:   Thu Feb 2 23:05:32 2017 +0100

    Further adaptions to get rid of fermi-lite fork
---
 debian/patches/adapt_to_debian_fermi-lite.patch |  2 +-
 debian/patches/fermi-lite_additional.h.patch    | 36 +++++++++++++++++++++++++
 debian/patches/fix_fermi-lite_usage.patch       |  3 ++-
 debian/patches/fix_missing_declaration.patch    | 11 --------
 debian/patches/fml_include_path.patch           | 33 +++++++++++++++++++++++
 debian/patches/series                           |  4 +--
 6 files changed, 74 insertions(+), 15 deletions(-)

diff --git a/debian/patches/adapt_to_debian_fermi-lite.patch b/debian/patches/adapt_to_debian_fermi-lite.patch
index 4d7a8ee..447467d 100644
--- a/debian/patches/adapt_to_debian_fermi-lite.patch
+++ b/debian/patches/adapt_to_debian_fermi-lite.patch
@@ -32,7 +32,7 @@ Description: In Debian's fermi-lite 0.1-3 a name space pollution with
  */
  
  #include "SeqLib/BFC.h"
-+#include <bfc.h>
++#include <fml/bfc.h>
  
  #include <stdexcept>
  #include <algorithm>
diff --git a/debian/patches/fermi-lite_additional.h.patch b/debian/patches/fermi-lite_additional.h.patch
new file mode 100644
index 0000000..114a599
--- /dev/null
+++ b/debian/patches/fermi-lite_additional.h.patch
@@ -0,0 +1,36 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
+Description: Upstream has put this into fermi-lite fork but as long this
+ is not accepted upstream we keep this here
+
+--- /dev/null
++++ b/src/fml_additional.h
+@@ -0,0 +1,18 @@
++#ifndef AC_FML_ADDITIONAL_H__
++#define AC_FML_ADDITIONAL_H__
++
++#include <fml/bfc.h>
++
++void kmer_correct(ec_step_t * es, int mode, bfc_ch_t * ch) {
++  int i = 0;
++  es->e = (bfc_ec1buf_t**)calloc(es->opt->n_threads, sizeof(void*)); //jwala added cast
++  for (i = 0; i < es->opt->n_threads; ++i)
++    es->e[i] = ec1buf_init(es->opt, ch), es->e[i]->mode = mode;
++  kt_for(es->opt->n_threads, worker_ec, es, es->n_seqs);
++  for (i = 0; i < es->opt->n_threads; ++i)
++    ec1buf_destroy(es->e[i]);
++  free(es->e);
++}
++
++#endif
++
+--- a/src/BFC.cpp
++++ b/src/BFC.cpp
+@@ -32,6 +32,7 @@ SOFTWARE.
+ 
+ #include "SeqLib/BFC.h"
+ #include <fml/bfc.h>
++#include "fml_additional.h"
+ 
+ #include <stdexcept>
+ #include <algorithm>
diff --git a/debian/patches/fix_fermi-lite_usage.patch b/debian/patches/fix_fermi-lite_usage.patch
index 9b2ec81..37da9aa 100644
--- a/debian/patches/fix_fermi-lite_usage.patch
+++ b/debian/patches/fix_fermi-lite_usage.patch
@@ -7,13 +7,14 @@ Description: Upstream tries to include a header file bfc.h which
 
 --- a/SeqLib/BFC.h
 +++ b/SeqLib/BFC.h
-@@ -2,8 +2,7 @@
+@@ -2,8 +2,8 @@
  #define SEQLIB_BFC_H
  
  extern "C" {
 -  #include "fermi-lite/bfc.h"
 -  #include "fermi-lite/fml.h"
 +  #include <fml.h>
++  #include <fml/bfc.h>
  }
  
  #include "SeqLib/BamRecord.h"
diff --git a/debian/patches/fix_missing_declaration.patch b/debian/patches/fix_missing_declaration.patch
deleted file mode 100644
index de6b94c..0000000
--- a/debian/patches/fix_missing_declaration.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- 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/fml_include_path.patch b/debian/patches/fml_include_path.patch
new file mode 100644
index 0000000..a4d3e65
--- /dev/null
+++ b/debian/patches/fml_include_path.patch
@@ -0,0 +1,33 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 27 Jan 2017 13:18:48 +0100
+Description: Make sure header files will be found in /usr/include/fml
+
+--- a/seq_test/Makefile.am
++++ b/seq_test/Makefile.am
+@@ -2,14 +2,11 @@ bin_PROGRAMS = seq_test
+ 
+ seq_test_CPPFLAGS = \
+      -I../src \
+-     -I../htslib \
++     -I/usr/include/fml \
+      -I.. \
+-     -I../fermi-lite --coverage
++     --coverage
+ 
+ seq_test_LDADD = \
+-	../fermi-lite/libfml.a \
+-	../bwa/libbwa.a \
+-	../htslib/libhts.a \
+ 	-lboost_unit_test_framework -lboost_system -lboost_timer -lboost_chrono
+ 
+ seq_test_LDFLAGS = --coverage
+--- a/src/Makefile.am
++++ b/src/Makefile.am
+@@ -1,6 +1,6 @@
+ noinst_LIBRARIES = libseqlib.a
+ 
+-libseqlib_a_CPPFLAGS = -I../ -I../htslib -Wno-sign-compare
++libseqlib_a_CPPFLAGS = -I../ -I/usr/include/fml -Wno-sign-compare
+ 
+ libseqlib_a_SOURCES =   FastqReader.cpp BFC.cpp ReadFilter.cpp SeqPlot.cpp jsoncpp.cpp ssw_cpp.cpp ssw.c \
+ 			GenomicRegion.cpp RefGenome.cpp BamWriter.cpp BamReader.cpp \
diff --git a/debian/patches/series b/debian/patches/series
index 04f0f2c..135d02c 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -2,5 +2,5 @@ use_debian_packaged_libs.patch
 adapt_to_debian_fermi-lite.patch
 fix_fermi-lite_usage.patch
 fix_htslib_usage.patch
-# remove_duplicated_typedefs.patch
-# fix_missing_declaration.patch
+fermi-lite_additional.h.patch
+fml_include_path.patch

-- 
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