Package: sift / 4.0.3b-4

Metadata

Package Version Patches format
sift 4.0.3b-4 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
fix_perl_interpreter_and_lib_path | (download)

SIFT_for_submitting_fasta_seq.csh.pod | 55 55 + 0 - 0 !
bin/Classify_SNPs_Indels.pl | 2 1 + 1 - 0 !
bin/SIFT_exome_indels.pl | 8 5 + 3 - 0 !
bin/SIFT_exome_nssnvs.pl | 10 7 + 3 - 0 !
bin/SIFT_for_submitting_NCBI_gi_id.csh | 51 27 + 24 - 0 !
bin/SIFT_for_submitting_fasta_seq.csh | 35 21 + 14 - 0 !
bin/SIFT_intersect_cds.pl | 2 1 + 1 - 0 !
bin/SNPClassifier/Classify_SNPs.pl | 2 1 + 1 - 0 !
bin/SNPClassifier/Extract_Coding_Info.pl | 2 1 + 1 - 0 !
bin/detect_indel.pl | 2 1 + 1 - 0 !
bin/detect_repeat.pl | 2 1 + 1 - 0 !
bin/get_sequences.pl | 2 1 + 1 - 0 !
bin/indelfile_to_gff.pl | 2 1 + 1 - 0 !
bin/map_coords_to_bin.pl | 2 1 + 1 - 0 !
bin/map_coords_to_bin_indels.pl | 2 1 + 1 - 0 !
bin/model_transcript.pl | 2 1 + 1 - 0 !
bin/perlscripts/get_BLINK_seq.pl | 2 1 + 1 - 0 !
bin/reformat_chrfile.pl | 2 1 + 1 - 0 !
bin/seqs_chosen_via_median_info.csh | 80 49 + 31 - 0 !
bin/sift_feed_to_chr_coords_batch.pl | 2 1 + 1 - 0 !
bin/snv_db_engine.pl | 5 3 + 2 - 0 !
info_on_seqs.pod | 46 46 + 0 - 0 !
src/Alignment.c | 25 16 + 9 - 0 !
src/Clumping.c | 4 2 + 2 - 0 !
src/Makefile | 45 45 + 0 - 0 !
src/Matrix_Info.c | 32 16 + 16 - 0 !
src/PN_blocks.c | 2 1 + 1 - 0 !
src/PN_convert.c | 323 167 + 156 - 0 !
src/Protdist.c | 2 1 + 1 - 0 !
src/Psiblast.c | 73 36 + 37 - 0 !
src/SortList.c | 2 1 + 1 - 0 !
src/blocklist.c | 2 1 + 1 - 0 !
src/choose_seqs_via_psiblastseedmedian.c | 132 66 + 66 - 0 !
src/clump_output_alignedseq.c | 6 3 + 3 - 0 !
src/consensus_to_seq.c | 6 3 + 3 - 0 !
src/info_on_seqs.c | 34 17 + 17 - 0 !
src/psiblast_res_to_fasta_dbpairwise.c | 33 17 + 16 - 0 !
src/seqs_from_psiblast_res.c | 12 6 + 6 - 0 !
src/sift_blimps.h | 12 12 + 0 - 0 !
39 files changed, 637 insertions(+), 426 deletions(-)

---
ld as needed | (download)

src/Makefile | 6 4 + 2 - 0 !
1 file changed, 4 insertions(+), 2 deletions(-)

 src/makefile patch
 [Michael Bienia]
 As sift fails to link with ld --as-needed, I had to patch src/Makefile
 to fix it. While at it I've also added support for dpkg-buildflags to
 use in CFLAGS and LDFLAGS.
 [Laszlo Kajan]
 Added dpkg-buildflags to CPPFLAGS.
 Michael's explicit $(BIN) rule is made unnecessary by using LDLIBS instead
 of his LIBS, as LDLIBS get used by the implicit make rules and achieves the
 same result.
fix_gcc_warnings | (download)

src/Alignment.c | 6 3 + 3 - 0 !
src/Matrix_Info.c | 2 1 + 1 - 0 !
src/PN_convert.c | 2 1 + 1 - 0 !
src/Psiblast.c | 8 4 + 4 - 0 !
src/clump_output_alignedseq.c | 2 1 + 1 - 0 !
5 files changed, 10 insertions(+), 10 deletions(-)

 fix gcc warnings.
jarfile | (download)

bin/IntersectLocations.sh | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 path to intersectfeatures.jar
 IntersectFeatures.jar file now in /usr/share, patch for calling script.