checkin

1 files changed, 65 insertions, 30 deletions

diff --git a/sys/libbio/fasta.c b/sys/libbio/fasta.c
index 6b40e99..078325a 100644
--- a/sys/libbio/fasta.c
+++ b/sys/libbio/fasta.c
@@ -40,8 +40,8 @@ grow(struct SeqBuf **sb, int min)
     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");
+    if(new = mem.alloc(heap, 1, sizeof(*new)+newcap), !new) {
+        errorf("memory: could not allocate new buffer\n");
         return 1;
     }
 
@@ -63,13 +63,13 @@ put(struct SeqBuf **sb, byte c)
     struct SeqBuf *sq;
 
     sq = *sb;
-    if (sq->it < (sq->b + sq->cap)) {
+    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");
+    if(err = grow(sb, 1), err) {
+        errorf("memory fail: could not allocate more buffer\n");
         sq->mem.free(sq->heap, sq);
         return 1;
     }
@@ -85,21 +85,11 @@ push(struct SeqBuf **sb, int n, void *buf)
     int d, err;
     struct SeqBuf *seq;
 
-    char *cb = buf;
-    for(d=0; d < n; d++) {
-        if(cb[d] == 0) {
-            printf("ERROR: zero byte being copied @ pos %d/%d\n", d, n);
-            printf("ERROR: string afterwards is %s\n", cb+n+1);
-            printf("ERROR: string afterwards is %s\n", cb+n+2);
-            exit(1);
-        }
-    }
-
     seq = *sb;
-    if(d = seq->cap - (seq->it - seq->b), d < n) {
-        assert(d > 0);
+    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");
+            errorf("memory fail: could not allocate more buffer\n");
             seq->mem.free(seq->heap, seq);
             return 1;
         }
@@ -137,7 +127,7 @@ fill(bio·SeqReader *rdr)
 
     n = rdr->rdr.read(rdr->io, 1, arrlen(rdr->buf), rdr->buf);
     if(n < 0) {
-        errorf("read: no data obtained from reader");
+        errorf("read: no data obtained from reader\n");
         return 1;
     }
     rdr->b    = rdr->buf;
@@ -166,7 +156,7 @@ bio·openseq(io·Reader rdr, void *io, mem·Allocator mem, void *heap)
     r->seq->cap  = INIT_NM_SIZE + INIT_SQ_SIZE;
 
     if (err=fill(r), err) {
-        errorf("fill: could not populate buffer");
+        errorf("fill: could not populate buffer\n");
         goto ERROR;
     }
 
@@ -209,7 +199,7 @@ readfasta(bio·SeqReader *rdr, bio·Seq *seq, byte hdr, byte stop)
     // 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--);
+        errorf("fasta/q format: expected '%c', found '%c'\n", hdr, *rdr->b--);
         return 1;
     }
 
@@ -224,7 +214,7 @@ NAME:
     push(&rdr->seq, rdr->b - beg, beg);
 
     if(err=fill(rdr), err) {
-        errorf("read: could not populate buffer");
+        errorf("read: could not populate buffer\n");
         return 1;
     }
     goto NAME;
@@ -246,16 +236,18 @@ SEQLOOP:
 
         rdr->b++;
     }
+#if 0
     for(byte *cb = rdr->seq->b+rdr->seq->off; cb != rdr->seq->it; ++cb) {
         if(*cb == 0) {
             printf("ERROR @ pos=%ld: Found zero byte\n", cb - rdr->seq->b+rdr->seq->off);
         }
     }
+#endif
 
     push(&rdr->seq, rdr->b - beg, beg);
 
     if(err=fill(rdr), err) {
-        errorf("read: could not populate buffer");
+        errorf("read: could not populate buffer\n");
         return 1;
     }
     goto SEQLOOP;
@@ -278,13 +270,13 @@ bio·readfasta(bio·SeqReader *rdr, bio·Seq *seq)
 
     err = readfasta(rdr, seq, '>', '>');
     if(err && err != EOF) {
-        errorf("parse fail: could not read sequence of record");
+        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;
+    seq->len  = rdr->seq->it - seq->s - 1; // shift by 1 as we pushed a '0' to end
     seq->q    = nil;
 
     return err;
@@ -303,14 +295,14 @@ bio·readfastq(bio·SeqReader *rdr, bio·Seq *seq)
 
     err = readfasta(rdr, seq, '@', '+');
     if(err) {
-        errorf("parse fail: could not read sequence of record");
+        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");
+        errorf("format error: no '+' character seperator found\n");
         return -1;
     }
 
@@ -323,7 +315,7 @@ EATLN:
     }
 
     if(err = fill((bio·SeqReader*)rdr), err) {
-        errorf("read: could not populate buffer");
+        errorf("read: could not populate buffer\n");
         return 1;
     }
     goto EATLN;
@@ -347,7 +339,7 @@ QUAL:
     push(&rdr->seq, rdr->b - beg, beg);
 
     if(err = fill((bio·SeqReader*)rdr), err) {
-        errorf("read: could not populate buffer");
+        errorf("read: could not populate buffer\n");
         return 1;
     }
     goto QUAL;
@@ -358,8 +350,51 @@ SUCCESS:
     put(&rdr->seq,  '\0');
 
     seq->name = rdr->seq->b;
-    seq->s    = rdr->seq->b + rdr->seq->off;
+    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;
+}