IndexFactory.writeIndex is incorrect for tabix indexes, missing BlockCompressedOutputStream

[akiezun]

IndexFactory.writeIndex is incorrect for tabix indexes (does not use BlockCompressedOutputStream) and thus loading the index will blow up (reading does use BlockCompressedInoutStream).

Courtesy of @droazen, we know that compressing the index is indeed the right thing:
"the tbi index itself is supposed to be block compressed. Cf., eg., the code for writing tbi indices in htslib (https://github.com/samtools/htslib/blob/1e2ed48935a58845cecb64880e8cf7553c7db852/hts.c):

} else if (fmt == HTS_FMT_TBI) {
    BGZF *fp = bgzf_open(fnidx, "w");
    if (fp == NULL) return -1;
    bgzf_write(fp, "TBI\1", 4);
    hts_idx_save_core(idx, fp, HTS_FMT_TBI);
    bgzf_close(fp);

"

gatk has a workaround: broadinstitute/gatk#1422

[magicDGS]

I think that this could be close, couldn't it?