Class: Minimap2::Native::FastxReader

Inherits:
Object
  • Object
show all
Defined in:
ext/ruby_minimap2/ruby_minimap2.c

Instance Method Summary collapse

Constructor Details

#initialize(path) ⇒ Object 



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# File 'ext/ruby_minimap2/ruby_minimap2.c', line 900

static VALUE fastx_initialize(VALUE self, VALUE path)
{
    rb_mm2_fastx_t *reader;
    VALUE path_string = rb_get_path(path);
    const char *path_ptr = StringValueCStr(path_string);
    int first;
    TypedData_Get_Struct(self, rb_mm2_fastx_t, &fastx_type, reader);
    if (strcmp(path_ptr, "-") == 0) {
#ifdef _WIN32
        int fd = _dup(_fileno(stdin));
        if (fd >= 0) _setmode(fd, _O_BINARY);
#else
        int fd = dup(fileno(stdin));
#endif
        if (fd >= 0) {
            reader->file = gzdopen(fd, "r");
            if (!reader->file) {
#ifdef _WIN32
                _close(fd);
#else
                close(fd);
#endif
            }
        }
    } else {
        reader->file = gzopen(path_ptr, "r");
    }
    if (!reader->file) rb_raise(eMinimap2Error, "Cannot open FASTA/FASTQ file: %s", StringValueCStr(path_string));
    first = gzgetc(reader->file);
    if (first != '>' && first != '@') {
        gzclose(reader->file);
        reader->file = NULL;
        rb_raise(eMinimap2Error, "Invalid FASTA/FASTQ file: %s", path_ptr);
    }
    if (gzungetc(first, reader->file) == -1) {
        gzclose(reader->file);
        reader->file = NULL;
        rb_raise(eMinimap2Error, "Cannot read FASTA/FASTQ file: %s", path_ptr);
    }
    reader->seq = kseq_init(reader->file);
    if (!reader->seq) {
        gzclose(reader->file);
        reader->file = NULL;
        rb_raise(eMinimap2Error, "Cannot initialize FASTA/FASTQ reader");
    }
    reader->closed = 0;
#ifdef RUBY_MINIMAP2_TESTING
    ++live_fastx_readers;
#endif
    return self;
}

Instance Method Details

#close ⇒ Object 



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# File 'ext/ruby_minimap2/ruby_minimap2.c', line 981

static VALUE fastx_close(VALUE self)
{
    rb_mm2_fastx_t *reader;
    TypedData_Get_Struct(self, rb_mm2_fastx_t, &fastx_type, reader);
    fastx_close_native(reader);
    return Qnil;
}

#next_record(read_comment) ⇒ Object 



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# File 'ext/ruby_minimap2/ruby_minimap2.c', line 952

static VALUE fastx_next(VALUE self, VALUE read_comment)
{
    rb_mm2_fastx_t *reader;
    VALUE result;
    int status;
    TypedData_Get_Struct(self, rb_mm2_fastx_t, &fastx_type, reader);
    if (reader->closed) return Qnil;
    status = kseq_read(reader->seq);
    if (status == -1) {
        fastx_close_native(reader);
        return Qnil;
    }
    if (status < -1) {
        fastx_close_native(reader);
        rb_raise(eMinimap2Error, "Malformed FASTA/FASTQ record");
    }
    if (reader->seq->name.l == 0 || reader->seq->seq.l == 0) {
        fastx_close_native(reader);
        rb_raise(eMinimap2Error, "Malformed FASTA/FASTQ record");
    }
    result = rb_ary_new_capa(RTEST(read_comment) ? 4 : 3);
    rb_ary_push(result, rb_str_new(reader->seq->name.s, reader->seq->name.l));
    rb_ary_push(result, rb_str_new(reader->seq->seq.s, reader->seq->seq.l));
    rb_ary_push(result, reader->seq->qual.l > 0 ? rb_str_new(reader->seq->qual.s, reader->seq->qual.l) : Qnil);
    if (RTEST(read_comment))
        rb_ary_push(result, reader->seq->comment.l > 0 ? rb_str_new(reader->seq->comment.s, reader->seq->comment.l) : Qnil);
    return result;
}