Author: tille Date: 2016-04-28 18:52:15 +0000 (Thu, 28 Apr 2016) New Revision: 21800
Modified: trunk/packages/seqprep/trunk/debian/changelog trunk/packages/seqprep/trunk/debian/control trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch trunk/packages/seqprep/trunk/debian/patches/hardening.patch trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch Log: New upstream version Modified: trunk/packages/seqprep/trunk/debian/changelog =================================================================== --- trunk/packages/seqprep/trunk/debian/changelog 2016-04-28 10:38:34 UTC (rev 21799) +++ trunk/packages/seqprep/trunk/debian/changelog 2016-04-28 18:52:15 UTC (rev 21800) @@ -1,3 +1,9 @@ +seqprep (1.2-1) unstable; urgency=medium + + * New upstream version + + -- Andreas Tille <[email protected]> Thu, 28 Apr 2016 20:36:22 +0200 + seqprep (1.1-6) unstable; urgency=medium * Add missing Python dependency to tests (Thanks for the patch to Modified: trunk/packages/seqprep/trunk/debian/control =================================================================== --- trunk/packages/seqprep/trunk/debian/control 2016-04-28 10:38:34 UTC (rev 21799) +++ trunk/packages/seqprep/trunk/debian/control 2016-04-28 18:52:15 UTC (rev 21800) @@ -9,7 +9,7 @@ python-markdown, ruby-ronn, zlib1g-dev -Standards-Version: 3.9.7 +Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/seqprep/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/seqprep/trunk/ Homepage: http://seqanswers.com/wiki/SeqPrep Modified: trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch =================================================================== --- trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch 2016-04-28 10:38:34 UTC (rev 21799) +++ trunk/packages/seqprep/trunk/debian/patches/fix_unused_variable_errors.patch 2016-04-28 18:52:15 UTC (rev 21800) @@ -5,8 +5,8 @@ --- a/SeqPrep.c +++ b/SeqPrep.c -@@ -67,7 +67,7 @@ - fprintf(stderr, "\t-X <read alignment maximum fraction gap cutoff; default = %f>\n", DEF_READ_GAP_FRAC_CUTOFF ); +@@ -68,7 +68,7 @@ void help ( char *prog_name ) { + fprintf(stderr, "\t-z <use mask; N will replace adapters>\n"); fprintf(stderr, "Optional Arguments for Merging:\n" ); fprintf(stderr, "\t-y <maximum quality score in output ((phred 33) default = '%c' )>\n", maximum_quality ); - fprintf(stderr, "\t-g <print overhang when adapters are present and stripped (use this if reads are different length)>\n"); @@ -14,16 +14,16 @@ fprintf(stderr, "\t-s <perform merging and output the merged reads to this file>\n" ); fprintf(stderr, "\t-E <write pretty alignments to this file for visual Examination>\n" ); fprintf(stderr, "\t-x <max number of pretty alignments to write (if -E provided); default = %d>\n", DEF_MAX_PRETTY_PRINT ); -@@ -133,7 +133,7 @@ +@@ -120,7 +120,7 @@ int main( int argc, char* argv[] ) { char reverse_discard_fn[MAX_FN_LEN]; char merged_out_fn[MAX_FN_LEN]; bool do_read_merging = false; - bool print_overhang = false; +// bool print_overhang = false; bool write_discard=false; + bool use_mask=false; char forward_primer[MAX_SEQ_LEN+1]; - strcpy(forward_primer, DEF_FORWARD_PRIMER); //set default -@@ -270,7 +270,8 @@ +@@ -261,7 +261,8 @@ int main( int argc, char* argv[] ) { maximum_quality = optarg[0]; break; case 'g' : @@ -35,7 +35,7 @@ do_read_merging = true; --- a/stdaln.c +++ b/stdaln.c -@@ -545,13 +545,12 @@ +@@ -545,13 +545,12 @@ int aln_local_core(unsigned char *seq1, int start, end, max_score; int thres, *suba, *ss; @@ -50,7 +50,7 @@ score_matrix = ap->matrix; N_MATRIX_ROW = ap->row; thres = _thres > 0? _thres : -_thres; -@@ -865,7 +864,7 @@ +@@ -865,7 +864,7 @@ uint16_t *aln_path2cigar(const path_t *p int aln_extend_core(unsigned char *seq1, int len1, unsigned char *seq2, int len2, const AlnParam *ap, path_t *path, int *path_len, int G0, uint8_t *_mem) { @@ -59,7 +59,7 @@ int32_t **s_array, *score_array; int is_overflow, of_base; uint32_t *eh; -@@ -892,7 +891,6 @@ +@@ -892,7 +891,6 @@ int aln_extend_core(unsigned char *seq1, s_array[i] = (int32_t*)_p, _p += 4 * len1; /* initialization */ aln_init_score_array(seq1, len1, N_MATRIX_ROW, score_matrix, s_array); Modified: trunk/packages/seqprep/trunk/debian/patches/hardening.patch =================================================================== --- trunk/packages/seqprep/trunk/debian/patches/hardening.patch 2016-04-28 10:38:34 UTC (rev 21799) +++ trunk/packages/seqprep/trunk/debian/patches/hardening.patch 2016-04-28 18:52:15 UTC (rev 21800) @@ -4,10 +4,9 @@ --- a/Makefile +++ b/Makefile -@@ -1,8 +1,8 @@ - CC=gcc --CFLAGS=-c -Wall -Werror -O0 -g -+CFLAGS+=-c -Wall -Werror -O0 -g +@@ -1,7 +1,7 @@ +-CFLAGS=-c -Wall -O0 -g -std=c99 ++CFLAGS+=-c -Wall -O0 -g -std=c99 #recommended options: -ffast-math -ftree-vectorize -march=core2 -mssse3 -O3 COPTS= -LDFLAGS=-lz -lm Modified: trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch =================================================================== --- trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch 2016-04-28 10:38:34 UTC (rev 21799) +++ trunk/packages/seqprep/trunk/debian/patches/replace-float-with-double.patch 2016-04-28 18:52:15 UTC (rev 21800) @@ -5,7 +5,7 @@ --- a/SeqPrep.c +++ b/SeqPrep.c -@@ -150,12 +150,12 @@ +@@ -138,12 +138,12 @@ int main( int argc, char* argv[] ) { int min_ol_adapter = DEF_OL2MERGE_ADAPTER; int min_ol_reads = DEF_OL2MERGE_READS; unsigned short int min_read_len =DEF_MIN_READ_LEN; @@ -23,7 +23,7 @@ unsigned short max_mismatch_adapter[MAX_SEQ_LEN+1]; unsigned short max_mismatch_reads[MAX_SEQ_LEN+1]; unsigned short min_match_adapter[MAX_SEQ_LEN+1]; -@@ -316,10 +316,10 @@ +@@ -307,10 +307,10 @@ int main( int argc, char* argv[] ) { //Calculate table matching overlap length to min matches and max mismatches for(i=0;i<MAX_SEQ_LEN+1;i++){ _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
