sci-biology/amos: bring in upstream patch to cope with secondary alignments from 'bwa mem -M'

Package-Manager: portage-2.2.18

8 files changed, 201 insertions, 0 deletions

diff --git a/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
new file mode 100644
index 000000000..300868f52
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 5c6cb92..b99bedd 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ 
+ # Checks for header files.
+ AC_CHECK_HEADERS([dlfcn.h fcntl.h float.h limits.h \
diff --git a/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
new file mode 100644
index 000000000..42066f7f2
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 506ea0c..a0a403c 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -15,6 +15,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
new file mode 100644
index 000000000..cb7dfb08a
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.3-samtoafg.patch
@@ -0,0 +1,40 @@
+Hello,
+
+I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
+Amos source repository. I find this very useful for coercing output from 
+assemblers which which don't track read location into amos by remapping 
+reads against the assembly and converting to afg - not ideal but better 
+than nothing when you don't have the 'real' read locations to work with.
+
+This fails, however when reads are aligned with 'bwa mem', which can 
+output multi-part alignments. sam2afg checks for reuse of the same read 
+id (presumably to prevent the generation of non-unique eid values), 
+consequently encountering multiple alignments for a read causes it to die.
+
+The following one-line patch allows sam2afg to skip these secondary 
+alignments present in 'bwa mem' output, provided bwa mem has been run 
+with the '-M' argument which sets the SAM 'secondary alignment' flag on 
+the alignments in question.
+
+Hopefully this will also be of use to others...
+
+Best Regards,
+James
+
+-- 
+Dr. James Abbott
+Lead Bioinformatician
+Bioinformatics Support Service
+Imperial College, London
+
+
+--- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
++++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
+@@ -105,6 +105,7 @@
+ 	die unless defined $qqual;
+ 
+ 	$tstart--; # convert to zero-based coordinate
++        next if $flag & 0x100; # secondary alignment
+ 	$qid .= "/1" if $flag & 0x40; #FREAD1
+ 	$qid .= "/2" if $flag & 0x80; #FREAD2
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
new file mode 100644
index 000000000..c2cc35c31
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 1a169cf..36cc05b 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -16,6 +16,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
new file mode 100644
index 000000000..cb7dfb08a
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.4-samtoafg.patch
@@ -0,0 +1,40 @@
+Hello,
+
+I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
+Amos source repository. I find this very useful for coercing output from 
+assemblers which which don't track read location into amos by remapping 
+reads against the assembly and converting to afg - not ideal but better 
+than nothing when you don't have the 'real' read locations to work with.
+
+This fails, however when reads are aligned with 'bwa mem', which can 
+output multi-part alignments. sam2afg checks for reuse of the same read 
+id (presumably to prevent the generation of non-unique eid values), 
+consequently encountering multiple alignments for a read causes it to die.
+
+The following one-line patch allows sam2afg to skip these secondary 
+alignments present in 'bwa mem' output, provided bwa mem has been run 
+with the '-M' argument which sets the SAM 'secondary alignment' flag on 
+the alignments in question.
+
+Hopefully this will also be of use to others...
+
+Best Regards,
+James
+
+-- 
+Dr. James Abbott
+Lead Bioinformatician
+Bioinformatics Support Service
+Imperial College, London
+
+
+--- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
++++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
+@@ -105,6 +105,7 @@
+ 	die unless defined $qqual;
+ 
+ 	$tstart--; # convert to zero-based coordinate
++        next if $flag & 0x100; # secondary alignment
+ 	$qid .= "/1" if $flag & 0x40; #FREAD1
+ 	$qid .= "/2" if $flag & 0x80; #FREAD2
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
new file mode 100644
index 000000000..158e9b126
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-ac_prog_ar.patch
@@ -0,0 +1,18 @@
+ configure.ac | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/configure.ac b/configure.ac
+index 9d4bb66..aa94364 100644
+--- a/configure.ac
++++ b/configure.ac
+@@ -12,6 +12,10 @@ AC_PROG_CPP
+ AC_PROG_CXX
+ AC_PROG_INSTALL
+ AC_PROG_RANLIB
++AN_MAKEVAR([AR], [AC_PROG_AR])
++AN_PROGRAM([ar], [AC_PROG_AR])
++AC_DEFUN([AC_PROG_AR], [AC_CHECK_TOOL(AR, ar, :)])
++AC_PROG_AR
+ AC_CHECK_TOOL(GHC, ghc)
+ AM_CONDITIONAL([HAVE_GHC], [test "$GHC"])
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
new file mode 100644
index 000000000..c2cc35c31
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-gcc-4.7.patch
@@ -0,0 +1,15 @@
+ ParseAligns/abyss-fixmate.cc |    1 +
+ 1 files changed, 1 insertions(+), 0 deletions(-)
+
+diff --git a/ParseAligns/abyss-fixmate.cc b/ParseAligns/abyss-fixmate.cc
+index 1a169cf..36cc05b 100644
+--- a/ParseAligns/abyss-fixmate.cc
++++ b/ParseAligns/abyss-fixmate.cc
+@@ -16,6 +16,7 @@
+ #include <iterator>
+ #include <sstream>
+ #include <string>
++#include <unistd.h>
+ 
+ using namespace std;
+ 
diff --git a/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
new file mode 100644
index 000000000..cb7dfb08a
--- /dev/null
+++ b/sci-biology/abyss/files/abyss-1.3.6-samtoafg.patch
@@ -0,0 +1,40 @@
+Hello,
+
+I see Shaun Jackmans' (abyss-)sam2afg script is available within the 
+Amos source repository. I find this very useful for coercing output from 
+assemblers which which don't track read location into amos by remapping 
+reads against the assembly and converting to afg - not ideal but better 
+than nothing when you don't have the 'real' read locations to work with.
+
+This fails, however when reads are aligned with 'bwa mem', which can 
+output multi-part alignments. sam2afg checks for reuse of the same read 
+id (presumably to prevent the generation of non-unique eid values), 
+consequently encountering multiple alignments for a read causes it to die.
+
+The following one-line patch allows sam2afg to skip these secondary 
+alignments present in 'bwa mem' output, provided bwa mem has been run 
+with the '-M' argument which sets the SAM 'secondary alignment' flag on 
+the alignments in question.
+
+Hopefully this will also be of use to others...
+
+Best Regards,
+James
+
+-- 
+Dr. James Abbott
+Lead Bioinformatician
+Bioinformatics Support Service
+Imperial College, London
+
+
+--- abyss-1.3.6/bin/abyss-samtoafg.ori	2015-05-23 23:43:46.797747928 +0200
++++ abyss-1.3.6/bin/abyss-samtoafg	2015-05-23 23:44:09.227747743 +0200
+@@ -105,6 +105,7 @@
+ 	die unless defined $qqual;
+ 
+ 	$tstart--; # convert to zero-based coordinate
++        next if $flag & 0x100; # secondary alignment
+ 	$qid .= "/1" if $flag & 0x40; #FREAD1
+ 	$qid .= "/2" if $flag & 0x80; #FREAD2
+