[med-svn] [psortb] 06/08: Adapt to hmmer2 interface

[Andreas Tille]

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tille pushed a commit to branch master
in repository psortb.

commit accaccd8861fee14f49dcc04013134f501f60d85
Author: Andreas Tille <tille at debian.org>
Date:   Wed Apr 12 21:00:37 2017 +0200

    Adapt to hmmer2 interface
---
 debian/control                           |  2 +-
 debian/patches/fix_hmmer_interface.patch | 20 ++++++++++++++++++++
 debian/patches/series                    |  1 +
 3 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 923a885..0398ed8 100644
--- a/debian/control
+++ b/debian/control
@@ -6,7 +6,7 @@ Priority: optional
 Build-Depends: debhelper (>= 10),
                bioperl,
                ncbi-blast+-legacy,
-               libsquid-dev,
+               libsquid-dev (>= 1.9g+cvs20050121-9~),
                libhmmer2-dev,
                pkg-config
 Standards-Version: 3.9.8
diff --git a/debian/patches/fix_hmmer_interface.patch b/debian/patches/fix_hmmer_interface.patch
new file mode 100644
index 0000000..6b65eb7
--- /dev/null
+++ b/debian/patches/fix_hmmer_interface.patch
@@ -0,0 +1,20 @@
+--- a/algorithm-hmm/hmm-binding.cpp
++++ b/algorithm-hmm/hmm-binding.cpp
+@@ -71,7 +71,7 @@ int HMM::load(char *filename) {
+   if(strlen(filename) == 0) return -1;
+ 
+   // Load the model from the specified file.
+-  if((hmmfp = HMMFileOpen(filename, "HMMERDB")) == NULL) return -1;
++  if((hmmfp = HMMFileOpen(filename, (char *)"HMMERDB")) == NULL) return -1;
+ 
+   if(! HMMFileRead(hmmfp, &tmp_model)) {
+     HMMFileClose(hmmfp);
+@@ -107,7 +107,7 @@ HMMReport *HMM::search(char *seq) {
+   if((model == NULL) ||(seq == NULL) || (!(seqlen = strlen(seq)))) return NULL;
+ 
+   // Convert the sequence to the format the HMMER library expects.
+-  dseq = DigitizeSequence(seq, seqlen);
++  dseq = DigitizeSequence((char *)seq, seqlen);
+ 
+   // Calculate the raw scores for the sequence.
+   if (P7ViterbiSize(seqlen, model->M) <= RAMLIMIT)
diff --git a/debian/patches/series b/debian/patches/series
index e334345..86dc063 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 biosquid_includes.patch
+fix_hmmer_interface.patch

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