Fastq defline parsing doesn't always work

[Robert Leach]

USE CASE: WHAT DO YOU WANT TO DO?

Match IDs in deflines up to the read ID.

STEPS TO REPRODUCE AN ISSUE (OR TRIGGER A NEW FEATURE)

1. Run the tests

CURRENT BEHAVIOR

Test 2 outputs this error:

‌ ERROR: Index ID mismatch: @HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 3:N:0: does not match @HWI-X00000:2:000000000-XXXXX:1:1117:19643:1028 1:N:0:
EXPECTED BEHAVIOR
Those IDs match and the reads should go into the file for BC4
DEVELOPERS ONLY SE_CTION
SUGGESTED CHANGE (Pseudocode opt_i_onal)_
Change this pattern match:

'(?P<instrument>[a-zA-Z0-9_-]+):'
'(?P<run_number>[0-9]+):'
'(?P<flowcell_id>[a-zA-Z0-9-]+):'
'(?P<lane>[0-9]+):(?P<tile>[0-9]+):'
'(?P<x_pos>[0-9]+):'
'(?P<y_pos>[0-9]+) (?P<read>[0-9]+):'
'(?P<is_filtered>[YN]):'
'(?P<control_number>[0-9]+):'
'(?P<index_sequence>[ACGT]+){0,1}'

LEVEL OF EFFORT
minor
COMMENTS

[Robert Leach]

Wow, the text editing interface on bitbucket has gotten much worse. So many difficulties in entering text.