forked from Lainports/opnsense-ports
8cb1a96ede
Taken from: https://github.com/freebsd/freebsd-ports.git Commit id: 5070672073b68be364139bc6b3a89100bd17d331
82 lines
1.9 KiB
C
82 lines
1.9 KiB
C
--- ./qual.c.orig 2008-11-12 17:45:48.000000000 +0100
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+++ ./qual.c 2014-08-02 12:39:30.000000000 +0200
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@@ -44,6 +44,12 @@
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static int mismatch_LLR[256];
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double *scaled_err_probs; /* used for finding high-quality segments */
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+void read_qual(Database *);
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+void rescale_qual(Database *);
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+void incr_diff_hist(unsigned char *, unsigned char *,
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+ int, int, int, int,
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+ int, int, int, int );
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+
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init_qual_arrays()
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{
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int i;
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@@ -580,6 +586,7 @@
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}
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/* read in quality data */
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+void
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read_qual(db)
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Database *db;
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{
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@@ -876,6 +883,7 @@
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}
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/* NOT CORRECT WITH COMPRESSED QUAL */
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+void
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rescale_qual(db)
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Database *db;
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{
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@@ -1153,6 +1161,10 @@
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int conf_count[2], conf_max_score, conf_max_margin; /* # confirming reads */
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} Diffsegnode;
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+void append_diffdata(Diffsegnode *);
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+void append_diffsegnode(Diffsegnode *, int, int, int, int, Diffsegnode *);
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+void write_diffsegnode(Diffsegnode *);
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+
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int data_type, data_length, data_qual, data_reverse, data_score, data_margin;
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unsigned char *data_seq;
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@@ -1400,6 +1412,7 @@
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= n_align[i] = n_unalign[i] = n_p_unalign[i] = 0;
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}
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+void
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incr_diff_hist(seq, diff, length1, length2, start1, start2, end1, end2, reverse, ignore_ends)
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unsigned char *seq;
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unsigned char *diff;
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@@ -1543,6 +1556,7 @@
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int node_index;
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extern unsigned char area_comp_mat[];
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+void
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append_diffdata(diffsegnode)
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Diffsegnode *diffsegnode;
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{
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@@ -1607,6 +1621,7 @@
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diffdata->count[!data_reverse] = 0;
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}
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+void
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append_diffsegnode(node, entry, seg_start, seg_end, conf_flag, data_node)
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Diffsegnode *node, *data_node; /* latter is 0 if reading from global vars */
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int entry, seg_start, seg_end, conf_flag;
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@@ -1724,6 +1739,7 @@
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strcpy(cdb, "CDSILRdi");
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}
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+void
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write_diffsegnode(node)
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Diffsegnode *node;
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{
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@@ -1800,6 +1816,7 @@
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write_diffsegnode(node->child[1]);
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}
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+void
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write_diffsegnodes()
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{
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int i;
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