This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository psortb.
commit b91dba4b157ec52eba705c32ee58e4395e2d72ce Author: Andreas Tille <[email protected]> Date: Wed Apr 12 22:24:03 2017 +0200 Adapt to hmmer2 interface --- debian/patches/fix_hmmer_interface.patch | 24 +++++++++++++++++++++++- 1 file changed, 23 insertions(+), 1 deletion(-) diff --git a/debian/patches/fix_hmmer_interface.patch b/debian/patches/fix_hmmer_interface.patch index 6b65eb7..4dba247 100644 --- a/debian/patches/fix_hmmer_interface.patch +++ b/debian/patches/fix_hmmer_interface.patch @@ -9,7 +9,21 @@ if(! HMMFileRead(hmmfp, &tmp_model)) { HMMFileClose(hmmfp); -@@ -107,7 +107,7 @@ HMMReport *HMM::search(char *seq) { +@@ -95,25 +95,26 @@ int HMM::load(char *filename) { + + HMMReport *HMM::search(char *seq) { + struct tophit_s *ghit, *dhit; ++ struct dpmatrix_s *mx; + struct p7trace_s *trace; + double pvalue, evalue; + int numhits; + HMMReport *hmmrep; + float score; + int seqlen; +- char *dseq; ++ unsigned char *dseq; + + // Ensure we have a valid model and sequence. if((model == NULL) ||(seq == NULL) || (!(seqlen = strlen(seq)))) return NULL; // Convert the sequence to the format the HMMER library expects. @@ -18,3 +32,11 @@ // Calculate the raw scores for the sequence. if (P7ViterbiSize(seqlen, model->M) <= RAMLIMIT) +- score = P7Viterbi(dseq, seqlen, model, &trace); ++ score = P7Viterbi(dseq, seqlen, model, mx, &trace); + else +- score = P7SmallViterbi(dseq, seqlen, model, &trace); ++ score = P7SmallViterbi(dseq, seqlen, model, mx, &trace); + + + // Calculate the score using the forward algorithm if we need. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/psortb.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
