Commit 6136085e authored by Afif Elghraoui's avatar Afif Elghraoui
Browse files

New upstream version 0.14.1+ds

parent 5aa6792b

NEWS

+12 −0
Original line number Diff line number Diff line
@@ -5,6 +5,18 @@ http://pysam.readthedocs.io/en/latest/release.html 
Release notes

=============



Release 0.14.1

==============



This is mostly a bugfix release, though bcftools has now also been

upgraded to 1.7.0.



* [#621] Add a warning to count_coverage when an alignment has an

  empty QUAL field

* [#635] Speed-up of AlignedSegment.find_intro()

* treat border case of all bases in pileup column below quality score

* [#634] Fix access to pileup reference_sequence



Release 0.14.0

==============

bcftools/bcftools.h

+17 −0
Original line number Diff line number Diff line
@@ -63,6 +63,23 @@ static inline char gt2iupac(char a, char b) 
    return iupac[(int)a][(int)b];

}



static inline int iupac_consistent(char iupac, char nt)

{

    static const char iupac_mask[90] = {

        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

        0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,14,2,

        13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,0,7,9,0,10

    };

    if ( iupac > 89 ) return 0;

    if ( nt > 90 ) nt -=  32;  // lowercase 

    if ( nt=='A' ) nt = 1;

    else if ( nt=='C' ) nt = 2;

    else if ( nt=='G' ) nt = 4;

    else if ( nt=='T' ) nt = 8;

    return iupac_mask[(int)iupac] & nt ? 1 : 0;

}



static inline char nt_to_upper(char nt)

{

    if ( nt < 97 ) return nt;

bcftools/consensus.c

+9 −4
Original line number Diff line number Diff line
@@ -77,6 +77,7 @@ typedef struct 
    rbuf_t vcf_rbuf;

    bcf1_t **vcf_buf;

    int nvcf_buf, rid;

    char *chr;



    regidx_t *mask;

    regitr_t *itr;
@@ -121,6 +122,8 @@ static void destroy_chain(args_t *args) 
    free(chain->block_lengths);

    free(chain);

    chain = NULL;

    free(args->chr);

    args->chr = NULL;

}



static void print_chain(args_t *args)
@@ -162,7 +165,7 @@ static void print_chain(args_t *args) 
        score += chain->block_lengths[n];

    }

    score += last_block_size;

    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, bcf_hdr_id2name(args->hdr,args->rid), ref_end_pos, chain->ori_pos, ref_end_pos, bcf_hdr_id2name(args->hdr,args->rid), alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);

    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);

    for (n=0; n<chain->num; n++) {

        fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]);

    }
@@ -248,6 +251,7 @@ static void destroy_data(args_t *args) 
        if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]);

    free(args->vcf_buf);

    free(args->fa_buf.s);

    free(args->chr);

    if ( args->mask ) regidx_destroy(args->mask);

    if ( args->itr ) regitr_destroy(args->itr);

    if ( args->chain_fname )
@@ -276,6 +280,7 @@ static void init_region(args_t *args, char *line) 
            else to--;

        }

    }

    args->chr = strdup(line);

    args->rid = bcf_hdr_name2id(args->hdr,line);

    if ( args->rid<0 ) fprintf(stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname);

    args->fa_buf.l = 0;
@@ -380,7 +385,7 @@ static void apply_variant(args_t *args, bcf1_t *rec) 
        if ( regidx_overlap(args->mask, chr,start,end,NULL) ) return;

    }



    int i, ialt = 1;

    int i, ialt = 1;    // the alternate allele

    if ( args->isample >= 0 )

    {

        bcf_unpack(rec, BCF_UN_FMT);
@@ -417,6 +422,7 @@ static void apply_variant(args_t *args, bcf1_t *rec) 
            {

                char ial = rec->d.allele[ialt][0];

                char jal = rec->d.allele[jalt][0];

                if ( !ialt ) ialt = jalt;   // only ialt is used, make sure 0/1 is not ignored

                rec->d.allele[ialt][0] = gt2iupac(ial,jal);

            }

        }
@@ -565,11 +571,10 @@ static void apply_variant(args_t *args, bcf1_t *rec) 


static void mask_region(args_t *args, char *seq, int len)

{

    char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);

    int start = args->fa_src_pos - len;

    int end   = args->fa_src_pos;



    if ( !regidx_overlap(args->mask, chr,start,end, args->itr) ) return;

    if ( !regidx_overlap(args->mask, args->chr,start,end, args->itr) ) return;



    int idx_start, idx_end, i;

    while ( regitr_overlap(args->itr) )

bcftools/consensus.c.pysam.c

+9 −4
Original line number Diff line number Diff line
@@ -79,6 +79,7 @@ typedef struct 
    rbuf_t vcf_rbuf;

    bcf1_t **vcf_buf;

    int nvcf_buf, rid;

    char *chr;



    regidx_t *mask;

    regitr_t *itr;
@@ -123,6 +124,8 @@ static void destroy_chain(args_t *args) 
    free(chain->block_lengths);

    free(chain);

    chain = NULL;

    free(args->chr);

    args->chr = NULL;

}



static void print_chain(args_t *args)
@@ -164,7 +167,7 @@ static void print_chain(args_t *args) 
        score += chain->block_lengths[n];

    }

    score += last_block_size;

    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, bcf_hdr_id2name(args->hdr,args->rid), ref_end_pos, chain->ori_pos, ref_end_pos, bcf_hdr_id2name(args->hdr,args->rid), alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);

    fprintf(args->fp_chain, "chain %d %s %d + %d %d %s %d + %d %d %d\n", score, args->chr, ref_end_pos, chain->ori_pos, ref_end_pos, args->chr, alt_end_pos, chain->ori_pos, alt_end_pos, ++args->chain_id);

    for (n=0; n<chain->num; n++) {

        fprintf(args->fp_chain, "%d %d %d\n", chain->block_lengths[n], chain->ref_gaps[n], chain->alt_gaps[n]);

    }
@@ -250,6 +253,7 @@ static void destroy_data(args_t *args) 
        if ( args->vcf_buf[i] ) bcf_destroy1(args->vcf_buf[i]);

    free(args->vcf_buf);

    free(args->fa_buf.s);

    free(args->chr);

    if ( args->mask ) regidx_destroy(args->mask);

    if ( args->itr ) regitr_destroy(args->itr);

    if ( args->chain_fname )
@@ -278,6 +282,7 @@ static void init_region(args_t *args, char *line) 
            else to--;

        }

    }

    args->chr = strdup(line);

    args->rid = bcf_hdr_name2id(args->hdr,line);

    if ( args->rid<0 ) fprintf(bcftools_stderr,"Warning: Sequence \"%s\" not in %s\n", line,args->fname);

    args->fa_buf.l = 0;
@@ -382,7 +387,7 @@ static void apply_variant(args_t *args, bcf1_t *rec) 
        if ( regidx_overlap(args->mask, chr,start,end,NULL) ) return;

    }



    int i, ialt = 1;

    int i, ialt = 1;    // the alternate allele

    if ( args->isample >= 0 )

    {

        bcf_unpack(rec, BCF_UN_FMT);
@@ -419,6 +424,7 @@ static void apply_variant(args_t *args, bcf1_t *rec) 
            {

                char ial = rec->d.allele[ialt][0];

                char jal = rec->d.allele[jalt][0];

                if ( !ialt ) ialt = jalt;   // only ialt is used, make sure 0/1 is not ignored

                rec->d.allele[ialt][0] = gt2iupac(ial,jal);

            }

        }
@@ -567,11 +573,10 @@ static void apply_variant(args_t *args, bcf1_t *rec) 


static void mask_region(args_t *args, char *seq, int len)

{

    char *chr = (char*)bcf_hdr_id2name(args->hdr,args->rid);

    int start = args->fa_src_pos - len;

    int end   = args->fa_src_pos;



    if ( !regidx_overlap(args->mask, chr,start,end, args->itr) ) return;

    if ( !regidx_overlap(args->mask, args->chr,start,end, args->itr) ) return;



    int idx_start, idx_end, i;

    while ( regitr_overlap(args->itr) )

bcftools/convert.c

+29 −1
Original line number Diff line number Diff line 
/*  convert.c -- functions for converting between VCF/BCF and related formats.



    Copyright (C) 2013-2017 Genome Research Ltd.

    Copyright (C) 2013-2018 Genome Research Ltd.



    Author: Petr Danecek <pd3@sanger.ac.uk>
@@ -92,6 +92,7 @@ struct _convert_t 
    int ndat;

    char *undef_info_tag;

    int allow_undef_tags;

    uint8_t **subset_samples;

};



typedef struct
@@ -174,6 +175,24 @@ static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx) 
    }

    return ((int32_t*)bcf_array)[idx];

}

static inline void _copy_field(char *src, uint32_t len, int idx, kstring_t *str)

{

    int n = 0, ibeg = 0;

    while ( src[ibeg] && ibeg<len && n < idx )

    {

        if ( src[ibeg]==',' ) n++;

        ibeg++;

    }

    if ( ibeg==len ) { kputc('.', str); return; }



    int iend = ibeg;

    while ( src[iend] && src[iend]!=',' && iend<len ) iend++;



    if ( iend>ibeg )

        kputsn(src+ibeg, iend-ibeg, str);

    else

        kputc('.', str);

}

static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)

{

    if ( fmt->id<0 )
@@ -232,6 +251,7 @@ static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isamp 
            case BCF_BT_INT16: BRANCH(int16_t, val==bcf_int16_missing, val==bcf_int16_vector_end, kputw(val, str)); break;

            case BCF_BT_INT32: BRANCH(int32_t, val==bcf_int32_missing, val==bcf_int32_vector_end, kputw(val, str)); break;

            case BCF_BT_FLOAT: BRANCH(float,   bcf_float_is_missing(val), bcf_float_is_vector_end(val), kputd(val, str)); break;

            case BCF_BT_CHAR:  _copy_field((char*)info->vptr, info->vptr_len, fmt->subscript, str); break;

            default: fprintf(stderr,"todo: type %d\n", info->type); exit(1); break;

        }

        #undef BRANCH
@@ -288,6 +308,8 @@ static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isa 
            else

                kputw(ival, str);

        }

        else if ( fmt->fmt->type == BCF_BT_CHAR )

            _copy_field((char*)(fmt->fmt->p + isample*fmt->fmt->size), fmt->fmt->size, fmt->subscript, str);

        else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);

    }

    else
@@ -1312,6 +1334,9 @@ int convert_line(convert_t *convert, bcf1_t *line, kstring_t *str) 
            }

            for (js=0; js<convert->nsamples; js++)

            {

                // Skip samples when filtering was requested

                if ( *convert->subset_samples && !(*convert->subset_samples)[js] ) continue;



                // Here comes a hack designed for TBCSQ. When running on large files,

                // such as 1000GP, there are too many empty fields in the output and

                // it's very very slow. Therefore in case the handler does not add
@@ -1362,6 +1387,9 @@ int convert_set_option(convert_t *convert, enum convert_option opt, ...) 
        case allow_undef_tags:

            convert->allow_undef_tags = va_arg(args, int);

            break;

        case subset_samples:

            convert->subset_samples = va_arg(args, uint8_t**);

            break;

        default:

            ret = -1;

    }