From 5d3642b8ef920316693031d2ea34b9def0b1abc5 Mon Sep 17 00:00:00 2001
From: Nicholas Noll <nbnoll@eml.cc>
Date: Thu, 22 Apr 2021 08:55:35 -0700
Subject: chore: rm unfinished projects

---
 sys/libbio/io/fasta.c | 360 --------------------------------------------------
 1 file changed, 360 deletions(-)
 delete mode 100644 sys/libbio/io/fasta.c

(limited to 'sys/libbio/io/fasta.c')

diff --git a/sys/libbio/io/fasta.c b/sys/libbio/io/fasta.c
deleted file mode 100644
index 28c9ca4..0000000
--- a/sys/libbio/io/fasta.c
+++ /dev/null
@@ -1,360 +0,0 @@
-#include <u.h>
-#include <libn.h>
-#include <libbio.h>
-
-#define INIT_NM_SIZE 128
-#define INIT_SQ_SIZE 4096
-
-struct Seqbuf 
-{
-    mem·Allocator heap;
-    void          *h;
-
-    int len;
-    int off;
-    byte   *it;
-    byte   b[];
-};
-
-static
-void
-reset(struct Seqbuf *sb)
-{
-    sb->off = 0;
-    sb->it  = sb->b;
-}
-
-static
-error
-grow(struct Seqbuf **sb, int min)
-{
-    struct Seqbuf *old, *new;
-    vlong newlen;
-
-    old = *sb;
-    assert((*sb)->len <= (SIZE_MAX - 1) / 2);
-    newlen = MAX(16, MAX(1 + 2*(*sb)->len, (*sb)->len+min));
-    assert(newlen >= (*sb)->len+min);
-
-    if (new = old->heap.alloc(old->h, 1, sizeof(*new)+newlen), !new) {
-        errorf("memory: could not allocate new buffer");
-        return 1;
-    }
-
-    memcpy(new, old, sizeof(*sb) + (*sb)->len);
-    new->len = newlen;
-    new->it  = new->b + (old->len); 
-    old->heap.free(old->h, old);
-
-    *sb = new;
-    return 0;
-}
-
-static
-error
-put(struct Seqbuf **sb, byte c)
-{
-    int err;
-    struct Seqbuf *sq;
-
-    sq = *sb;
-    if (sq->it < (sq->b + sq->len)) {
-        *sq->it++ = c;
-        return 0;
-    }
-
-    if (err = grow(sb, 1), err) {
-        errorf("memory fail: could not allocate more buffer");
-        sq->heap.free(sq->h, sq);
-        return 1;
-    }
-
-    *((*sb)->it++) = c;
-    return 0;
-}
-
-static
-error
-push(struct Seqbuf **sb, int n, void *buf)
-{
-    int d, err;
-    struct Seqbuf *seq;
-
-    seq = *sb;
-    if (d = seq->len - (seq->it - seq->b), d < n) {
-        assert(d > 0);
-        if (err = grow(sb, n-d), err) {
-            errorf("memory fail: could not allocate more buffer");
-            seq->heap.free(seq->h, seq);
-            return 1;
-        }
-    }
-
-    memcpy((*sb)->it, buf, n);
-    (*sb)->it += n;
-
-    return 0;
-}
-
-// -----------------------------------------------------------------------
-// Fasta files
-
-struct bio·FastaReader {
-    byte      eof;
-    io·Reader file;
-    void      *f;
-
-    struct Seqbuf *seq;
-
-    /* read buffer */
-    byte *b, *bend;
-    byte buf[4*4098];
-};
-
-static
-error
-fill(bio·FastaReader *rdr)
-{
-    int n;
-    // NOTE: This could lead to an infinite loop.
-    if (rdr->eof) {
-        return 0;
-    }
-
-    n = rdr->file.read(rdr->f, 1, arrlen(rdr->buf), rdr->buf);
-    if (n < 0) {
-        errorf("read: no data obtained from reader");
-        return 1;
-    }
-    rdr->b    = rdr->buf;
-    rdr->bend = rdr->b + n;
-    if (rdr->eof = n < arrlen(rdr->buf), rdr->eof) {
-        *rdr->bend++ = '\0';
-    }
-
-    return 0;
-}
-
-bio·FastaReader*
-bio·openfasta(io·Reader file, void *f, mem·Allocator heap, void *h)
-{
-    error err;
-    bio·FastaReader *rdr;
-
-    rdr = heap.alloc(h, 1, sizeof(bio·FastaReader));
-    rdr->file = file;
-    rdr->f    = f;
-    rdr->eof  = 0;
-
-    rdr->seq = heap.alloc(h, 1, sizeof(*rdr->seq) + INIT_NM_SIZE + INIT_SQ_SIZE);
-    rdr->seq->heap = heap;
-    rdr->seq->h    = h;
-    rdr->seq->it   = rdr->seq->b;
-    rdr->seq->len  = INIT_NM_SIZE + INIT_SQ_SIZE;
-
-    if (err = fill(rdr), err) {
-        errorf("fill: could not populate buffer");
-        goto ERROR;
-    }
-
-    return rdr;
-
-ERROR:
-    heap.free(h, rdr->seq);
-    heap.free(h, rdr);
-    return nil;
-}
-
-static
-error
-readfasta(bio·FastaReader *rdr, bio·Seq *seq, byte hdr, byte stop)
-{
-    error  err;
-    byte  *beg;
-    
-    if (rdr->eof && rdr->b == rdr->bend-1) {
-        return EOF;
-    }
-
-    reset(rdr->seq);
-
-    // NOTE: Can this case happen?
-    assert(rdr->b != rdr->bend);
-    if (*rdr->b++ != hdr) {
-        errorf("fasta/q format: expected '%c', found '%c'", hdr, *rdr->b--);
-        return 1;
-    }
-
-NAME:
-    beg = rdr->b;
-    while (rdr->b != rdr->bend) {
-        if (*rdr->b++ == '\n') {
-            push(&rdr->seq, (rdr->b - 1) - beg, beg);
-            goto SEQ;
-        }
-    }
-
-    push(&rdr->seq, rdr->b - beg, beg);
-
-    if (err = fill(rdr), err) {
-        errorf("read: could not populate buffer");
-        return 1;
-    }
-    goto NAME;
-
-SEQ:
-    put(&rdr->seq, '\0');
-    rdr->seq->off = rdr->seq->it - rdr->seq->b;
-
-SEQL:
-    beg = rdr->b;
-    while (rdr->b != rdr->bend) {
-        if (*rdr->b == '\n') {
-            push(&rdr->seq, rdr->b - beg, beg);
-            beg = rdr->b + 1;
-        }
-
-        if (*rdr->b == stop || *rdr->b == '\0') {
-            goto SUCCESS;
-        }
-
-        rdr->b++;
-    }
-
-    push(&rdr->seq, rdr->b - beg, beg);
-
-    if (err = fill(rdr), err) {
-        errorf("read: could not populate buffer");
-        return 1;
-    }
-    goto SEQL;
-
-SUCCESS:
-    push(&rdr->seq, rdr->b - beg, beg);
-    put(&rdr->seq, '\0');
-
-    return 0;
-}
-
-error
-bio·readfasta(bio·FastaReader *rdr, bio·Seq *seq)
-{
-    error err;
-
-    err = readfasta(rdr, seq, '>', '>');
-    if (err && err != EOF) {
-        errorf("parse fail: could not read sequence of record");
-        return err;
-    }
-
-    seq->name = rdr->seq->b;
-    seq->s    = rdr->seq->b + rdr->seq->off;
-    seq->len  = rdr->seq->it - seq->s;
-    seq->q    = nil;
-
-    return err;
-}
-
-error
-bio·closefasta(bio·FastaReader *rdr)
-{
-    mem·Allocator heap;
-    void         *h;
-
-    heap = rdr->seq->heap;
-    h    = rdr->seq->h; 
-    
-    heap.free(h, rdr->seq);
-    heap.free(h, rdr);
-
-    return 0;
-}
-
-// -----------------------------------------------------------------------
-// Fastq files
-
-struct bio·FastqReader {
-    struct bio·FastaReader;
-};
-
-bio·FastqReader*
-bio·openfastq(io·Reader file, void *f, mem·Allocator heap, void *h)
-{
-    return (bio·FastqReader*)bio·openfasta(file, f, heap, h);
-}
-
-error
-bio·closefastq(bio·FastqReader *rdr)
-{
-    return bio·closefasta((bio·FastaReader*)rdr);
-}
-
-error
-bio·readfastq(bio·FastqReader *rdr, bio·Seq *seq)
-{
-    int   n;
-    byte *beg;
-    error err;
-
-    err = readfasta((bio·FastaReader*)rdr, seq, '@', '+');
-    if (err) {
-        errorf("parse fail: could not read sequence of record");
-        return err;
-    }
-
-    seq->len = rdr->seq->it - (rdr->seq->b + rdr->seq->off);
-
-    if (*rdr->b++ != '+') {
-        errorf("format error: no '+' character seperator found");
-        return -1;
-    }
-
-EATLN:
-    while (rdr->b != rdr->bend) {
-        if (*rdr->b++ == '\n') {
-            n = 0;
-            goto QUAL;
-        }
-    }
-
-    if (err = fill((bio·FastaReader*)rdr), err) {
-        errorf("read: could not populate buffer");
-        return 1;
-    }
-    goto EATLN;
-
-QUAL:
-    beg = rdr->b;
-    while (rdr->b != rdr->bend) {
-        if (*rdr->b == '\n') {
-            push(&rdr->seq, rdr->b - beg, beg);
-            beg = rdr->b + 1;
-        }
-
-        if (n++ == seq->len || *rdr->b == '\0') {
-            err = *rdr->b == '\0' ? EOF : 0;
-            goto SUCCESS;
-        }
-
-        rdr->b++;
-    }
-
-    push(&rdr->seq, rdr->b - beg, beg);
-
-    if (err = fill((bio·FastaReader*)rdr), err) {
-        errorf("read: could not populate buffer");
-        return 1;
-    }
-    goto QUAL;
-
-
-SUCCESS:
-    push(&rdr->seq, rdr->b - beg, beg);
-    put(&rdr->seq,  '\0');
-
-    seq->name = rdr->seq->b;
-    seq->s    = rdr->seq->b + rdr->seq->off;
-    seq->q    = seq->s + seq->len + 1;
-
-    return err;
-}
-- 
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