biogo / hts

In func (r *ChunkReader) Read(p []byte) (int, error), I get:

panic: runtime error: slice bounds out of range

goroutine 1 [running]:
github.com/biogo/hts/bgzf/index.(*ChunkReader).Read(0xc208994270, 0xc20883d20c, 0xdf4, 0xdf4, 0x7f80307beaa8, 0x0, 0x0)
    /usr/local/src/gocode/src/github.com/biogo/hts/bgzf/index/index.go:64 +0x714
bufio.(*Reader).fill(0xc208e391a0)
    /usr/local/go/src/bufio/bufio.go:97 +0x1ce
bufio.(*Reader).ReadSlice(0xc208e391a0, 0xc20883d80a, 0x0, 0x0, 0x0, 0x0, 0x0)
    /usr/local/go/src/bufio/bufio.go:295 +0x257
bufio.(*Reader).ReadBytes(0xc208e391a0, 0xc2085c780a, 0x0, 0x0, 0x0, 0x0, 0x0)
    /usr/local/go/src/bufio/bufio.go:374 +0xd2
bufio.(*Reader).ReadString(0xc208e391a0, 0xa, 0x0, 0x0, 0x0, 0x0)
    /usr/local/go/src/bufio/bufio.go:414 +0x58
...

I printed out:

        log.Println(r.chunks[0].End.Block, r.r.LastChunk().End.Block, len(p))

in the offending if statement and see:

2015/09/06 07:41:48 64366 3148 3572

I'm hoping you see an obvious solution (maybe using vOffset() is required in the if?), otherwise, I'll try to make a small test-case.

I'm confused, line 64 of index.go is blank: https://github.com/biogo/hts/blob/master/bgzf/index/index.go#L64

However, the fix is obvious, I should be using min(len(p), r.chunks[0].End.Block-r.r.LastChunk().End.Block). Can you send a test case?

I can't seem to conjure up a small test-case. I'm actually iterating over ExAC when I get this. Making the change you suggest does fix.

I'll try to fake a test tomorrow.

Line 64 could suggest brentp is running 812fc97 Make Blocked API via field

hts/bgzf/index/index.go

Line 64 in 812fc97

}

It would be line 62 + 1 line for import log and 1 line for the log.Println() that I added.

panic from slice out of bounds in bgzf.index