removed buggy qsort header and implemented myself

1 files changed, 117 insertions, 0 deletions

diff --git a/sys/libbio/simulate.c b/sys/libbio/simulate.c
new file mode 100644
index 0000000..a4567d5
--- /dev/null
+++ b/sys/libbio/simulate.c
@@ -0,0 +1,117 @@
+#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]);
+    }
+}