Use hopen for non BAM files

[jenniferliddle]

Replace open() with hopen() throughout, so that we can open files directly from irods or AWS or Google web services.

This will involve replacing the existing XML library used by i2b

[dkj]

Like! But the XML library replacement sounds like possibly too high a cost.

[jenniferliddle]

I don't think so. I wouldn't be trying to write a generic XML parser, but a parser for known, specific XML config files. It shouldn't be too difficult.

[dkj]

Chatting to our colleagues fopencookie might provide a generic way of obtaining standard file handles from hfile.

[jenniferliddle]

Ah Ha!
libXML does provide a xmlParseMemory() function that I can use in place of xmlReadFile(). Which works.
Ok, so I don't get to write my own XML parser. I can live with that :-)

[dkj]

Need to avoid opendir and readdir but as this is only used for instrument file format detection we can probably just try obtaining the different file names/formats for tile1, lane <requested>||1, cycle1 .