690da7ea38
biology/phrab biology/phred biology/consed Although these programs are licensed freely for academic and nonprofit purposes, users have to contact the authors to obtain the tarballs. PR: 191336 Submitted by: mzaki@m.u-tokyo.ac.jp (maintainer)
88 lines
2.3 KiB
C
88 lines
2.3 KiB
C
--- ./analyze_splices.c.orig 2008-08-31 03:37:44.000000000 +0200
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+++ ./analyze_splices.c 2014-08-02 12:39:30.000000000 +0200
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@@ -146,6 +146,13 @@
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char *exon_seq;
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double base_llr, intron_coeff;
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+void find_left_sites(Aligned_pair *, Cand_pair *, char *, char *);
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+void find_right_sites(Aligned_pair *, Cand_pair *, char *, char *);
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+void increment_splice_site(unsigned char *, unsigned char *,
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+ Aligned_pair *, int, int, int, unsigned char *, int);
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+void scan(Splice_site *, Aligned_pair *, unsigned char *,
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+ int, int, int, int);
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+
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set_splice_params()
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{
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int i, j;
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@@ -186,6 +193,7 @@
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cases of large missing exons: want to make sure this part of read doesn't match somewhere else, instead
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*/
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+void
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append_cand_splice(strand, left_splice_site, right_splice_site, overlap, intron_length, left_pair, right_pair)
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int strand, overlap, intron_length;
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Splice_site *left_splice_site, *right_splice_site;
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@@ -512,6 +520,7 @@
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return penalty;
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}
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+void
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check_best_site(pair, side, cand_pair)
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Aligned_pair *pair;
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int side;
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@@ -560,6 +569,7 @@
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int extend[3];
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+void
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find_left_sites(pair, cand_pair, seq1, seq2)
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Aligned_pair *pair;
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Cand_pair *cand_pair;
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@@ -651,6 +661,7 @@
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}
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+void
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find_right_sites(pair, cand_pair, seq1, seq2)
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Aligned_pair *pair;
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Cand_pair *cand_pair;
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@@ -816,6 +827,7 @@
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This doesn't really address multiple testing issue;
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*/
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+void
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increment_splice_site(seq1, seq2, pair, strand, side, loc, seq, type)
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Aligned_pair *pair;
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int strand, side, loc, type;
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@@ -922,6 +934,7 @@
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/* input: splice_site, c_len, pair, seq1, exon_seq, genome_overhang, cdna_overhang, base_llr, intron_coeff, max_i */
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+void
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scan(splice_site, pair, seq1, genome_overhang, cdna_overhang, max_i, test_len)
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Splice_site *splice_site;
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Aligned_pair *pair;
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@@ -1098,6 +1111,7 @@
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return n_matches;
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}
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+void
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check_max_length(length)
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int length;
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{
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@@ -1118,6 +1132,7 @@
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max_length = length;
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}
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+void
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filter_matches(i_ptr, n_p, pair_pointers, print_flag)
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int i_ptr, n_p, print_flag;
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Aligned_pair **pair_pointers;
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@@ -1276,6 +1291,7 @@
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return seg_equiv1->start - seg_equiv2->start;
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}
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+void
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analyze_multiple(i_ptr, n_p, pair_pointers, print_flag)
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int i_ptr, n_p, print_flag;
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Aligned_pair **pair_pointers;
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