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Mpileup revamp #1474

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merged 16 commits into from
May 10, 2021
Merged

Mpileup revamp #1474

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d6176f9
Improve mpileup speed by delaying BAQ calculation.
jkbonfield Dec 17, 2020
8d790c8
Make a new calc_mwu_biasZ with s.d. normalised Z score.
jkbonfield Jan 19, 2021
b8d5468
Add an indel-bias argument to mpileup.
jkbonfield Feb 18, 2021
9d80d1e
Add indel BQBZ, MQBZ, RPBZ and SCBZ INFO fields.
jkbonfield Feb 19, 2021
00969a1
Improve the indel INFO filtering metric, plus big fix to GT accuracy.
jkbonfield Feb 25, 2021
474f77d
Addition of STR finder.
jkbonfield Apr 22, 2021
fe55d9f
Refactor bcf_call_gap_prep.
jkbonfield Mar 8, 2021
69a0941
Tidy up STR finder and fix iscore calc.
jkbonfield Mar 8, 2021
69c9e40
bam2bcf_indel tidyups.
jkbonfield Mar 9, 2021
91f76ca
Rewrite get_position to not parse entire CIGAR.
jkbonfield Mar 12, 2021
bed1774
Improve calling for PacBio CCS reads.
jkbonfield Mar 11, 2021
c3b75b5
Remove the second probaln_glocal call from the indel caller.
jkbonfield Mar 18, 2021
6e840fb
Adjust min/max qual for SNP caller.
jkbonfield Mar 22, 2021
e4e1610
Fix for REF/ALT indel calculation.
jkbonfield Apr 7, 2021
b842297
Add mpileup -U option for old MWU scale.
jkbonfield Apr 23, 2021
354b7b5
Make partial-BAQ the default in mpileup.
jkbonfield Apr 23, 2021
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25 changes: 25 additions & 0 deletions LICENSE
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Original file line number Diff line number Diff line change
Expand Up @@ -746,3 +746,28 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

-----------------------------------------------------------------------------

LICENSE for utlist.h

Copyright (c) 2007-2014, Troy D. Hanson http://troydhanson.github.com/uthash/
All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
5 changes: 3 additions & 2 deletions Makefile
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Expand Up @@ -42,7 +42,7 @@ OBJS = main.o vcfindex.o tabix.o \
regidx.o smpl_ilist.o csq.o vcfbuf.o \
mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
vcfsort.o cols.o extsort.o dist.o abuf.o \
ccall.o em.o prob1.o kmin.o
ccall.o em.o prob1.o kmin.o str_finder.o
PLUGIN_OBJS = vcfplugin.o

prefix = /usr/local
Expand Down Expand Up @@ -233,6 +233,7 @@ abuf_h = abuf.h $(htslib_vcf_h)
bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
bam_sample_h = bam_sample.h $(htslib_sam_h)

str_finder.o: str_finder.h utlist.h
main.o: main.c $(htslib_hts_h) config.h version.h $(bcftools_h)
vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h) $(convert_h) $(smpl_ilist_h) regidx.h $(htslib_khash_h)
vcfplugin.o: vcfplugin.c config.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) $(bcftools_h) vcmp.h $(filter_h)
Expand Down Expand Up @@ -275,7 +276,7 @@ regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib
consensus.o: consensus.c $(htslib_vcf_h) $(htslib_kstring_h) $(htslib_synced_bcf_reader_h) $(htslib_kseq_h) $(htslib_bgzf_h) regidx.h $(bcftools_h) rbuf.h $(filter_h)
mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
bam2bcf.o: bam2bcf.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h) mw.h
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h)
bam2bcf_indel.o: bam2bcf_indel.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h
bam_sample.o: bam_sample.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(khash_str2str_h) $(bam_sample_h) $(bcftools_h)
version.o: version.h version.c
hclust.o: hclust.c $(htslib_hts_h) $(htslib_kstring_h) $(bcftools_h) hclust.h
Expand Down
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