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Viewing changes to src/transcript_utils.c

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-13 15:04:19 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20140613150419-v49mxnlg42rnuks5
Tags: 1.16.3-1
* New upstream version
* New (Build-)Depends: r-bioc-genomeinfodb
* cme fix dpkg-control
* add autopkgtest

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Lines of Context:
src/transcript_utils.c
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}
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static int copy_exon(char * out, const cachedCharSeq *in,
 
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static int copy_exon(char * out, const Chars_holder *in,
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                int start, int end, int on_minus_strand, SEXP lkup)
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{
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        int width;
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        return width;
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}
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static void copy_transcript(char * out, const cachedCharSeq *in,
 
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static void copy_transcript(char * out, const Chars_holder *in,
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                SEXP starts, SEXP ends,
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                int on_minus_strand, int decreasing_rank_on_minus_strand,
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                SEXP lkup)
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                SEXP exonStarts, SEXP exonEnds, SEXP strand,
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                SEXP decreasing_rank_on_minus_strand, SEXP lkup)
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{
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        cachedCharSeq X, Y;
 
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        Chars_holder X, Y;
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        SEXP ans_width, ans, starts, ends;
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        cachedXVectorList cached_ans;
 
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        XVectorList_holder ans_holder;
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        int decreasing_rank_on_minus_strand0, ans_length,
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            i, on_minus_strand;
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        X = cache_XRaw(x);
 
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        X = hold_XRaw(x);
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        decreasing_rank_on_minus_strand0 =
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                LOGICAL(decreasing_rank_on_minus_strand)[0];
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        PROTECT(ans_width = mk_transcript_widths(exonStarts,
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                                        exonEnds, X.length));
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        PROTECT(ans = alloc_XRawList(CHAR(STRING_ELT(classname, 0)),
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                                        get_classname(x), ans_width));
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        cached_ans = cache_XVectorList(ans);
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        ans_length = get_cachedXVectorList_length(&cached_ans);
 
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        ans_holder = hold_XVectorList(ans);
 
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        ans_length = get_length_from_XVectorList_holder(&ans_holder);
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        for (i = 0; i < ans_length; i++) {
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                starts = VECTOR_ELT(exonStarts, i);
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                if (starts == R_NilValue || LENGTH(starts) == 0)
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                        UNPROTECT(2);
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                        error("%s", errmsg_buf);
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                }
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                Y = get_cachedXRawList_elt(&cached_ans, i);
 
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                Y = get_elt_from_XRawList_holder(&ans_holder, i);
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                /* Y.seq is a const char * so we need to cast it to
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                   char * before we can write to it */
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                copy_transcript((char *) Y.seq, &X,