From ce05175372a9ddca1a225db0765ace1127a39293 Mon Sep 17 00:00:00 2001
From: Nicholas <nbnoll@eml.cc>
Date: Fri, 12 Nov 2021 09:22:01 -0800
Subject: chore: simplified organizational structure

---
 sys/libbio/simulate.c | 120 --------------------------------------------------
 1 file changed, 120 deletions(-)
 delete mode 100644 sys/libbio/simulate.c

(limited to 'sys/libbio/simulate.c')

diff --git a/sys/libbio/simulate.c b/sys/libbio/simulate.c
deleted file mode 100644
index 0f5a97e..0000000
--- a/sys/libbio/simulate.c
+++ /dev/null
@@ -1,120 +0,0 @@
-#include <u.h>
-#include <libn.h>
-#include <libbio.h>
-
-#define SEQLEN 2560
-static byte *SEQ =
-"GGCGGCTTCGGTGCGCTGTGTGCATTGCCGCAAAAATATCGTGAACCCGTGCTGGTTTCCGGCACTGACGGCGTAGGTAC"
-"CAAGCTGCGTCTGGCAATGGACTTAAAACGTCACGACACCATTGGTATTGATCTGGTCGCCATGTGCGTTAATGACCTGG"
-"TGGTGCAAGGTGCGGAACCGCTGTTTTTCCTCGACTATTACGCAACCGGAAAACTGGATGTTGATACCGCTTCAGCGGTG"
-"ATCAGCGGCATTGCGGAAGGTTGTCTGCAATCGGGCTGTTCTCTGGTGGGTGGCGAAACGGCAGAAATGCCGGGGATGTA"
-"TCACGGTGAAGATTACGATGTCGCGGGTTTCTGCGTGGGCGTGGTAGAAAAATCAGAAATCATCGACGGCTCTAAAGTCA"
-"GCGACGGCGATGTGCTGATTGCACTCGGTTCCAGCGGTCCGCACTCGAACGGTTATTCGCTGGTGCGCAAAATTCTTGAA"
-"GTCAGCGGTTGTGATCCGCAAACCACCGAACTTGATGGTAAGCCATTAGCCGATCATCTGCTGGCACCGACCCGCATTTA"
-"CGTGAAGTCAGTGCTGGAGTTGATTGAAAAGGTCGATGTGCATGCCATTGCGCACCTGACCGGCGGCGGCTTCTGGGAAA"
-"ACATTCCGCGCGTATTGCCAGATAATACCCAGGCAGTGATTGATGAATCTTCCTGGCAGTGGCCGGAAGTGTTCAACTGG"
-"CTGCAAACGGCAGGTAACGTTGAGCGCCATGAAATGTATCGCACCTTCAACTGCGGCGTCGGGATGATTATCGCCCTGCC"
-"TGCTCCGGAAGTGGACAAAGCCCTCGCCCTGCTCAATGCCAACGGTGAAAACGCGTGGAAAATCGGTATCATCAAAGCCT"
-"CTGATTCCGAACAACGCGTGGTTATCGAATAATGAATATTGTGGTGCTTATTTCCGGCAACGGAAGTAATTTACAGGCAA"
-"TTATTGACGCCTGTAAAACCAACAAAATTAAAGGCACCGTACGGGCAGTTTTCAGCAATAAGGCCGACGCGTTCGGCCTT"
-"GAACGCGCCCGCCAGGCGGGTATTGCAACGCATACGCTCATCGCCAGCGCGTTTGACAGTCGTGAAGCCTATGACCGGGA"
-"GTTGATTCATGAAATCGACATGTACGCACCCGATGTGGTCGTGCTGGCTGGTTTTATGCGCATTCTCAGCCCGGCGTTTG"
-"TCTCCCACTATGCCGGGCGTTTGCTGAACATTCACCCTTCTCTGCTGCCGAAATATCCCGGATTACACACCCATCGTCAA"
-"GCGCTGGAAAATGGCGATGAAGAGCACGGTACATCGGTGCATTTCGTCACCGATGAACTGGACGGTGGCCCGGTTATTTT"
-"ACAGGCGAAAGTCCCGGTATTTGCTGGTGATACGGAAGATGACGTCACCGCCCGCGTGCAAACCCAGGAACACGCCATTT"
-"ATCCACTGGTGATTAGCTGGTTTGCCGATGGTCGTCTGAAAATGCACGAAAACGCCGCGTGGCTGGATGGTCAACGTCTG"
-"CCGCCGCAGGGCTACGCTGCCGACGAGTAATGCCCCCGTAGTTAAAGCGCCAGCTCTGCCGCTGGCGTTTTTCAATTCAC"
-"CTGTAAATCGCAAGCTCCAGCAGTTTTTTTCCCCCTTTTCTGGCATAGTTGGACATCTGCCAATATTGCTCGCCATAATA"
-"TCCAGGCAGTGTCCCGTGAATAAAACGGAGTAAAAGTGGTAATGGGTCAGGAAAAGCTATACATCGAAAAAGAGCTCAGT"
-"TGGTTATCGTTCAATGAACGCGTGCTTCAGGAAGCGGCGGACAAATCTAACCCGCTGATTGAAAGGATGCGTTTCCTGGG"
-"GATCTATTCCAATAACCTTGATGAGTTCTATAAAGTCCGCTTCGCTGAACTGAAGCGACGCATCATTATTAGCGAAGAAC"
-"AAGGCTCCAACTCTCATTCCCGCCATTTACTGGGCAAAATTCAGTCCCGGGTGCTGAAAGCCGATCAGGAATTCGACGGC"
-"CTCTACAACGAGCTATTGCTGGAGATGGCGCGCAACCAGATCTTCCTGATTAATGAACGCCAGCTCTCCGTCAATCAACA"
-"AAACTGGCTGCGTCATTATTTTAAGCAGTATCTGCGTCAGCACATTACGCCGATTTTAATCAATCCTGACACTGACTTAG"
-"TGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTTCTGGAG"
-"ATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGA"
-"TAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGA"
-"TGACCCGCGATGCCGAATACGATTTAGTGCATGAGATGGAAGCCAGCCTGATGGAGTTGATGTCTTCCAGTCTCAAGCAG"
-"CGTTTAACTGCTGAGCCGGTGCGTTTTGTTTATCAGCGCGATATGCCCAATGCGCTGGTTGAAGTTTTACGCGAAAAACT";
-
-byte*
-modify(byte *seq, int *len, double p)
-{
-    byte *head, *new;
-
-    head = calloc(SEQLEN+1, sizeof(byte));
-    new  = head;
-    for (; *seq != '\0'; seq++) {
-        if (rng·bernoulli(p)) {
-            switch (rng·randi(5)) {
-            case 0: *new++ = 'A'; break;
-            case 1: *new++ = 'C'; break;
-            case 2: *new++ = 'G'; break;
-            case 3: *new++ = 'T'; break;
-            case 4: continue;
-            }
-        } else {
-            *new++ = *seq;
-        }
-    }
-    *new = '\0';
-    *len = new - head;
-    return head;
-}
-
-#define NSEQS 20
-int
-main()
-{
-    int n, i, l, lens[NSEQS];
-    byte     *seqs[NSEQS];
-
-    int    locs[aln·N][NSEQS][aln·L];
-    int    *loc[aln·N];
-    uint64 vals[aln·N][NSEQS][aln·L];
-    uint64 *val[aln·N];
-
-    rng·init(0);
-
-    seqs[0] = SEQ;
-    lens[0] = SEQLEN;
-
-    for (n = 0; n < aln·N; n++) {
-        for (i = 0; i < NSEQS; i++) {
-            for (l = 0; l < aln·L; l++) {
-                vals[n][i][l] = 0;
-            }
-        }
-    }
-
-    for (i = 1; i < NSEQS; i++) {
-        seqs[i] = modify(SEQ, lens + i, .01*i);
-    }
-
-    for (i = 0; i < NSEQS; i++) {
-        for (n = 0; n < aln·N; n++) {
-            val[n] = vals[n][i];
-            loc[n] = locs[n][i];
-        }
-        aln·sketch(seqs[i], aln·L, val, loc);
-    }
-
-    // for (n = 0; n < aln·N; n++) {
-    //     printf("iteration %d\n", n);
-    //     printf("[\n");
-    //     for (i = 0; i < NSEQS; i++) {
-    //         printf("  [");
-    //         for (l = 0; l < aln·L; l++) {
-    //             printf("%lu,", vals[n][i][l]);
-    //         }
-    //         printf("],\n");
-    //     }
-    //     printf("]\n");
-    // }
-
-    for (n = 0; n < aln·N; n++) {
-        aln·sort(NSEQS, aln·L, (uint64*)vals[n]);
-    }
-
-    return 0;
-}
-- 
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