Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2015	Dec. 31, 2014	Dec. 31, 2013
Cash flows from operating activities:
Net loss	$ (81,177)	$ (53,916)	$ (162,013)
Adjustments to reconcile net loss to net cash used in operating activities:
Non-cash royalty revenue related to sale of future royalties	(22,058)	(21,937)	(22,055)
Non-cash interest expense on liability related to sale of future royalties	20,619	20,888	22,309
Stock-based compensation	19,669	17,017	17,708
Depreciation and amortization	12,855	12,927	14,275
Loss from redemption premium and incremental interest on 12% senior secured notes	12,500	0	0
Write-off of deferred financing costs on 12% senior secured notes	1,579	0	0
Other non-cash transactions	(2,365)	(560)	664
Changes in assets and liabilities:
Accounts receivable, net	(16,340)	(1,378)	3,576
Inventory	1,606	500	4,817
Other assets	(825)	(3,294)	6,423
Accounts payable	(412)	(6,359)	6,199
Accrued compensation	249	(8,505)	5,481
Accrued clinical trial expenses	512	(9,197)	(595)
Other accrued expenses	(2,278)	273	(1,915)
Interest payable	(2,719)	0	(166)
Deferred revenue	(17,530)	(4,664)	(12,399)
Liability related to receipt of refundable milestone payment	0	(70,000)	70,000
Other liabilities	3,032	(13,801)	9,164
Net cash used in operating activities	(73,083)	(142,006)	(38,527)
Cash flows from investing activities:
Purchases of investments	(297,608)	(297,251)	(268,068)
Maturities of investments	226,923	247,995	319,181
Sales of investments	42,544	21,661	2,887
Release of restricted cash	25,000	0	0
Purchases of property, plant and equipment	(11,195)	(9,976)	(4,091)
Net cash (used in) provided by investing activities	(14,336)	(37,571)	49,909
Cash flows from financing activities:
Payment of capital lease obligations	(5,187)	(3,536)	(2,992)
Proceeds from issuance of 7.75% senior secured notes, net of issuance costs	241,262	0	0
Repayment of 12% senior secured notes	(125,000)	0	0
Payment of redemption premium and incremental interest on 12% senior secured notes	(12,500)	0	0
Repayment of proceeds from sale of future royalties	0	(7,000)	(3,000)
Issuance of common stock, net of issuance costs	0	116,536	0
Proceeds from shares issued under equity compensation plans	32,208	46,984	8,208
Net cash provided by financing activities	130,783	152,984	2,216
Effect of exchange rates on cash and cash equivalents	(159)	(109)	32
Net increase (decrease) in cash and cash equivalents	43,205	(26,702)	13,630
Cash and cash equivalents at beginning of year	12,365	39,067	25,437
Cash and cash equivalents at end of year	55,570	12,365	39,067
Supplemental disclosure of cash flow information:
Cash paid for interest	20,225	17,445	17,590
Cash paid for income taxes	860	964	1,014
Supplemental schedule of non-cash investing and financing activities:
Property and equipment acquired through capital leases and other financing	$ 93	$ 5,231	$ 2,000