private static int reg2bins(final int beg, final int _end, final int[] list) {
int i = 0, k, end = _end;
+ if (beg >= end) return 0;
+ if (end >= 1<<29) end = 1<<29;
--end;
list[i++] = 0;
for (k = 1 + (beg>>26); k <= 1 + (end>>26); ++k) list[i++] = k;
private TIntv getIntv(final String s) {
TIntv intv = new TIntv();
int col = 0, end = 0, beg = 0;
- while ((end = s.indexOf('\t', beg)) >= 0) {
+ while ((end = s.indexOf('\t', beg)) >= 0 || end == -1) {
++col;
if (col == mSc) {
intv.tid = chr2tid(s.substring(beg, end));
else --intv.beg;
if (intv.beg < 0) intv.beg = 0;
if (intv.end < 1) intv.end = 1;
- } else { // FIXME: SAM/VCF supports are not tested yet
+ } else { // FIXME: SAM supports are not tested yet
if ((mPreset&0xffff) == 0) { // generic
if (col == mEc)
intv.end = Integer.parseInt(s.substring(beg, end));
intv.end = intv.beg + l;
}
} else if ((mPreset&0xffff) == 2) { // VCF
- if (col == 5) {
- String alt = s.substring(beg, end);
- int i, max = 1;
- for (i = 0; i < alt.length(); ++i) {
- if (alt.charAt(i) == 'D') { // deletion
- int j;
- for (j = i; j < alt.length() && alt.charAt(j) >= '0' && alt.charAt(j) <= '9'; ++j);
- int l = Integer.parseInt(alt.substring(i, j));
- if (max < l) max = l;
- i = j - 1;
- }
+ String alt;
+ alt = end >= 0? s.substring(beg, end) : s.substring(beg);
+ if (col == 4) { // REF
+ if (alt.length() > 0) intv.end = intv.beg + alt.length();
+ } else if (col == 8) { // INFO
+ int e_off = -1, i = alt.indexOf("END=");
+ if (i == 0) e_off = 4;
+ else if (i > 0) {
+ i = alt.indexOf(";END=");
+ if (i >= 0) e_off = i + 5;
+ }
+ if (e_off > 0) {
+ i = alt.indexOf(";", e_off);
+ intv.end = Integer.parseInt(i > e_off? alt.substring(e_off, i) : alt.substring(e_off));
}
- intv.end = intv.beg + max;
}
}
}
+ if (end == -1) break;
beg = end + 1;
}
return intv;
TIndex idx = mIndex[tid];
int[] bins = new int[MAX_BIN];
int i, l, n_off, n_bins = reg2bins(beg, end, bins);
- min_off = (beg>>TAD_LIDX_SHIFT >= idx.l.length)? idx.l[idx.l.length-1] : idx.l[beg>>TAD_LIDX_SHIFT];
+ if (idx.l.length > 0)
+ min_off = (beg>>TAD_LIDX_SHIFT >= idx.l.length)? idx.l[idx.l.length-1] : idx.l[beg>>TAD_LIDX_SHIFT];
+ else min_off = 0;
for (i = n_off = 0; i < n_bins; ++i) {
if ((chunks = idx.b.get(bins[i])) != null)
n_off += chunks.length;