Bed track opening is too slow when file is on a SSHFS disk

[iromeo]

Bed track opening is too slow when file is on a SSHFS disk

E.g. try to open /mnt/stripe/bio/experiments/blueprint/data_redo/bp.all.covered.regions.hg19.filtered.mean10.bed.

IO reading speed is about 50-100 kb/s or less.

Probably it is caused by my current network connection conditions. Let's check it later.
Is related to #1302.

[iromeo]

Consider trying

fun Path.inputStream(vararg options: OpenOption) =
        FileInputStream(toFile()).buffered(32 * 1024).streamFor(name)

instead of

fun Path.inputStream(vararg options: OpenOption) =
        Files.newInputStream(this, *options).buffered().streamFor(name)

There are some reports that seek operation is slow while using Files.newInputStream(this, *options), althoug shouldn't affect us due to reading file from the begining up to end in Bed parser.

[iromeo]

Also, consider custom buffer size in BufferedReader / BufferedInputStream, the default value is 8 kb

[iromeo]

related: 2ad3a4619de0c5dd21ef83e342b2e95e05d75629