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/fasta.c | 393 -----------------------------------------------------
 1 file changed, 393 deletions(-)
 delete mode 100644 sys/libbio/fasta.c

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

diff --git a/sys/libbio/fasta.c b/sys/libbio/fasta.c
deleted file mode 100644
index 3788544..0000000
--- a/sys/libbio/fasta.c
+++ /dev/null
@@ -1,393 +0,0 @@
-#include <u.h>
-#include <base.h>
-#include <libbio.h>
-
-#define INIT_NM_SIZE 128
-#define INIT_SQ_SIZE 4096
-
-struct SeqBuf
-{
-    mem·Allocator mem;
-    void         *heap;
-
-    int  cap, off;
-    byte *it, b[];
-};
-
-static
-void
-reset(struct SeqBuf *sb)
-{
-    sb->off = 0;
-    sb->it  = sb->b;
-}
-
-static
-error
-grow(struct SeqBuf **sb, int min)
-{
-    void* heap;
-    mem·Allocator mem;
-
-    vlong newcap;
-    struct SeqBuf *old, *new;
-
-    old  = *sb;
-    mem  = old->mem;
-    heap = old->heap;
-
-    assert((*sb)->cap <= (SIZE_MAX - 1) / 2);
-    newcap = MAX(16, MAX(1 + 2*(*sb)->cap, (*sb)->cap+min));
-    assert(newcap >= (*sb)->cap+min);
-
-    if(new = mem.alloc(heap, 1, sizeof(*new)+newcap), !new) {
-        errorf("memory: could not allocate new buffer\n");
-        return 1;
-    }
-
-    memcpy(new, old, sizeof(*new) + (*sb)->cap);
-
-    new->cap = newcap;
-    new->it  = new->b + (old->it - old->b); 
-    mem.free(heap, 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->cap)) {
-        *sq->it++ = c;
-        return 0;
-    }
-
-    if(err = grow(sb, 1), err) {
-        errorf("memory fail: could not allocate more buffer\n");
-        sq->mem.free(sq->heap, 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->cap - (seq->it - seq->b)), d < n) {
-        assert(d >= 0);
-        if (err = grow(sb, n-d), err) {
-            errorf("memory fail: could not allocate more buffer\n");
-            seq->mem.free(seq->heap, seq);
-            return 1;
-        }
-    }
-    seq = *sb;
-
-    memcpy(seq->it, buf, n);
-    seq->it += n;
-
-    return 0;
-}
-
-// -----------------------------------------------------------------------
-// sequence data
-
-struct bio·SeqReader {
-    byte      eof;
-    io·Reader rdr;
-    void      *io;
-
-    struct SeqBuf *seq;
-
-    /* read buffer */
-    byte *b, *bend, buf[4*4098];
-};
-
-static
-error
-fill(bio·SeqReader *rdr)
-{
-    int n;
-    // NOTE: This could lead to an infinite loop.
-    if(rdr->eof)
-        return 0;
-
-    n = rdr->rdr.read(rdr->io, 1, arrlen(rdr->buf), rdr->buf);
-    if(n < 0) {
-        errorf("read: no data obtained from reader\n");
-        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·SeqReader*
-bio·openseq(io·Reader rdr, void *io, mem·Allocator mem, void *heap)
-{
-    error err;
-    bio·SeqReader *r;
-
-    r = mem.alloc(heap, 1, sizeof(bio·SeqReader));
-    r->rdr = rdr;
-    r->io  = io;
-    r->eof = 0;
-
-    r->seq = mem.alloc(heap, 1, sizeof(*r->seq) + INIT_NM_SIZE + INIT_SQ_SIZE);
-    r->seq->mem  = mem;
-    r->seq->heap = heap;
-    r->seq->it   = r->seq->b;
-    r->seq->cap  = INIT_NM_SIZE + INIT_SQ_SIZE;
-
-    if (err=fill(r), err) {
-        errorf("fill: could not populate buffer\n");
-        goto ERROR;
-    }
-
-    return r;
-
-ERROR:
-    mem.free(heap, r->seq);
-    mem.free(heap, r);
-    return nil;
-}
-
-error
-bio·closeseq(bio·SeqReader *rdr)
-{
-    mem·Allocator mem;
-    void         *heap;
-
-    mem  = rdr->seq->mem;
-    heap = rdr->seq->heap; 
-
-    mem.free(heap, rdr->seq);
-    mem.free(heap, rdr);
-
-    return 0;
-}
-
-
-static
-error
-readfasta(bio·SeqReader *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'\n", 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\n");
-        return 1;
-    }
-    goto NAME;
-
-SEQ:
-    put(&rdr->seq, '\0');
-    rdr->seq->off = rdr->seq->it - rdr->seq->b;
-
-SEQLOOP:
-    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\n");
-        return 1;
-    }
-    goto SEQLOOP;
-
-SUCCESS:
-    push(&rdr->seq, rdr->b - beg, beg);
-    put(&rdr->seq, '\0');
-
-    return 0;
-}
-
-/* 
- * fasta files
- */
-
-error
-bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq)
-{
-    error err;
-
-    err = readfasta(rdr, seq, '>', '>');
-    if(err && err != EOF) {
-        errorf("parse fail: could not read sequence of record\n");
-        return err;
-    }
-
-    seq->name = rdr->seq->b;
-    seq->s    = rdr->seq->b + rdr->seq->off;
-    seq->len  = rdr->seq->it - seq->s - 1; // shift by 1 as we pushed a '0' to end
-    seq->q    = nil;
-
-    return err;
-}
-
-/* 
- * fastq files
- */
-
-error
-bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq)
-{
-    int   n;
-    byte *beg;
-    error err;
-
-    err = readfasta(rdr, seq, '@', '+');
-    if(err) {
-        errorf("parse fail: could not read sequence of record\n");
-        return err;
-    }
-
-    seq->len = rdr->seq->it - (rdr->seq->b + rdr->seq->off);
-
-    if(*rdr->b++ != '+') {
-        errorf("format error: no '+' character seperator found\n");
-        return -1;
-    }
-
-EATLN:
-    while(rdr->b != rdr->bend) {
-        if (*rdr->b++ == '\n') {
-            n = 0;
-            goto QUAL;
-        }
-    }
-
-    if(err = fill((bio·SeqReader*)rdr), err) {
-        errorf("read: could not populate buffer\n");
-        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·SeqReader*)rdr), err) {
-        errorf("read: could not populate buffer\n");
-        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 - 1;
-    seq->q    = seq->s + seq->len + 1;
-
-    return err;
-}
-
-// -----------------------------------------------------------------------
-// sequence writing
-
-error 
-bio·writefasta(io·Writer io, void *wtr, bio·Seq seq)
-{
-    int i, j, d;
-    char buf[2048], *b = buf, *e = arrend(buf);
-
-    *b++ = '>';
-    while(*seq.name) {
-        *b++ = *seq.name++;
-        if(b == e) {
-            io.write(wtr, 1, arrlen(buf), buf);
-            b = buf;
-        }
-    }
-
-    for(i=0; i<seq.len; i = j) {
-        j = MIN(i+70, seq.len);
-        d = j - i;
-        if((e-b) <= d+1) {
-            io.write(wtr, 1, b-buf, buf);
-            b = buf;
-        }
-        *b++ = '\n';
-        memcpy(b, seq.s+i, d);
-        b += d;
-    }
-
-    *b++ = '\n';
-    io.write(wtr, 1, b-buf, buf);
-
-    return 0;
-}
-
-error
-bio·writefastq(io·Writer io, void *wtr, bio·Seq seq)
-{
-    panicf("need to implement");
-    return 1;
-}
-- 
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