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New mpileup2 draft (intended for discussions, not ready to merge!) #1842

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New mpileup2 draft (intended for discussions, not ready to merge!) #1842

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888c024
Backup commit only, nothing is working, long way to go
pd3 Sep 30, 2022
dc159df
Merge from develop, resolve conflicts
pd3 Nov 23, 2022
b53a611
Merge branch 'develop' into mpileup2
pd3 Nov 23, 2022
ed814e3
Backup commit. Compiles but not functional
pd3 Nov 23, 2022
3ef5f6a
Backup commit. Compiles but not functional
pd3 Nov 23, 2022
35b6e91
Merge branch 'mpileup2' of github.com:samtools/bcftools into mpileup2
pd3 Nov 25, 2022
a5aa714
Merge branch 'develop' into mpileup2
pd3 Nov 25, 2022
3c53fca
Backup commit
pd3 Nov 30, 2022
1b84cff
Merge branch 'develop' into mpileup2
pd3 Jan 16, 2023
8493d96
backup commit: finish regions vgr $bt mpileup2 -f test/mpileup/mpileu…
pd3 Jun 26, 2023
922a5f1
backup commit
pd3 Jul 11, 2023
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7 changes: 5 additions & 2 deletions Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,10 @@ OBJS = main.o vcfindex.o tabix.o \
vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
vcfcnv.o vcfhead.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o \
regidx.o smpl_ilist.o csq.o vcfbuf.o \
mpileup.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \
mpileup.o mpileup2.o bam2bcf.o bam2bcf_indel.o bam2bcf_iaux.o read_consensus.o bam_sample.o \
vcfsort.o cols.o extsort.o dist.o abuf.o \
ccall.o em.o prob1.o kmin.o str_finder.o
ccall.o em.o prob1.o kmin.o str_finder.o \
mpileup2/mpileup.o
PLUGIN_OBJS = vcfplugin.o

prefix = /usr/local
Expand Down Expand Up @@ -277,6 +278,8 @@ cols.o: cols.c cols.h
regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h
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) $(htslib_hts_os_h) regidx.h $(bcftools_h) $(bam2bcf_h) $(bam_sample_h) $(gvcf_h)
mpileup2.o: mpileup2.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_hts_os_h) $(bcftools_h) mpileup2/mpileup.h
mpileup2/mpileup.o: mpileup2/mpileup.h mpileup2/mpileup.c
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) str_finder.h
bam2bcf_iaux.o: bam2bcf_iaux.c $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_str2int_h) $(bam2bcf_h) $(htslib_ksort_h) str_finder.h read_consensus.h cigar_state.h
Expand Down
3 changes: 2 additions & 1 deletion bam2bcf.h
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Expand Up @@ -108,7 +108,8 @@ plp_cd_t;


typedef struct __bcf_callaux_t {
int fmt_flag, ambig_reads;
uint32_t fmt_flag;
int ambig_reads;
int capQ, min_baseQ, max_baseQ, delta_baseQ;
int openQ, extQ, tandemQ; // for indels
uint32_t min_support, max_support; // for collecting indel candidates
Expand Down
5 changes: 5 additions & 0 deletions main.c
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Expand Up @@ -61,6 +61,7 @@ int count_plugins(void);
int main_consensus(int argc, char *argv[]);
int main_csq(int argc, char *argv[]);
int main_mpileup(int argc, char *argv[]);
int main_mpileup2(int argc, char *argv[]);
int main_sort(int argc, char *argv[]);

typedef struct
Expand Down Expand Up @@ -174,6 +175,10 @@ static cmd_t cmds[] =
.alias = "mpileup",
.help = "multi-way pileup producing genotype likelihoods"
},
{ .func = main_mpileup2,
.alias = "mpileup2",
.help = "-new version of mpileup (experimental)" // do not advertise yet
},
#if USE_GPL
{ .func = main_polysomy,
.alias = "polysomy",
Expand Down
18 changes: 1 addition & 17 deletions mpileup.c
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Expand Up @@ -47,9 +47,6 @@ DEALINGS IN THE SOFTWARE. */
#include "bam_sample.h"
#include "gvcf.h"

#define MPLP_BCF 1
#define MPLP_VCF (1<<1)
#define MPLP_NO_COMP (1<<2)
#define MPLP_NO_ORPHAN (1<<3)
#define MPLP_REALN (1<<4)
#define MPLP_NO_INDEL (1<<5)
Expand Down Expand Up @@ -1078,7 +1075,7 @@ int read_file_list(const char *file_list,int *n,char **argv[])
continue; \
}

void parse_format_flag(uint32_t *flag, const char *str)
static void parse_format_flag(uint32_t *flag, const char *str)
{
int i, n_tags;
char **tags = hts_readlist(str, 0, &n_tags);
Expand Down Expand Up @@ -1562,19 +1559,6 @@ int main_mpileup(int argc, char *argv[])
fprintf(stderr,"[warning] The -a DP option is required with --gvcf, switching on.\n");
mplp.fmt_flag |= B2B_FMT_DP;
}
if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
{
if ( mplp.flag&MPLP_VCF )
{
if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF;
else mplp.output_type = FT_VCF_GZ;
}
else if ( mplp.flag&MPLP_BCF )
{
if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF;
else mplp.output_type = FT_BCF_GZ;
}
}
if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
{
fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
Expand Down
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