FASTQ sanity check

[edsu7]

FASTQ sanity check

[b-f-chan]

Concern: How long does this check take for "normal" or "average" sized input file?

Not a lot of workarounds for this; basically just checking size of a GZIP file --> Don't have tools to easily increase speed of this or would take a lot of work that's not worth it

Can do a quick benchmark test with a file to see how it takes; see if reasonable, then can merge PR

[b-f-chan]

On behalf of @edsu7 :

Based on below, it should take ~15 minutes for 600 million reads.

NOTE: Units are in minutes

File	# Reads	Time Rep1	Time Rep2	Time Rep3	Time Average
BIN67_BRG1_rep3_merged_R1.fastq.gz	77,877,363	3.46	1.45	1.44	2.116666667
BIN67_BRG1_rep3_merged_R2.fastq.gz	77,877,363	2	1.46	1.48	1.646666667
BIN67_CONTROL_rep2_merged_R1.fastq.gz	86,832,404	2.13	1.59	2.7	2.14
BIN67_CONTROL_rep2_merged_R2.fastq.gz	86,832,404	2.14	2	2.6	2.246666667
BIN67_CONTROL_rep4_merged_R1.fastq.gz	88,900,467	2.21	2	1.58	1.93
BIN67_CONTROL_rep4_merged_R2.fastq.gz	88,900,467	2.25	2.5	2.1	2.283333333
BIN67_BRG1_rep1_merged_R1.fastq.gz	91,202,472	2.3	2.2	2.3	2.266666667
BIN67_BRG1_rep1_merged_R2.fastq.gz	91,202,472	2.3	2.6	2.8	2.566666667
BIN67_CONTROL_rep3_merged_R1.fastq.gz	91,507,599	2.14	2.2	2.2	2.18
BIN67_CONTROL_rep3_merged_R2.fastq.gz	91,507,599	2.17	2.9	2.13	2.4
BIN67_BRG1_rep2_merged_R1.fastq.gz	99,933,061	2.44	2.15	2.15	2.246666667
BIN67_BRG1_rep2_merged_R2.fastq.gz	99,933,061	2.51	2.16	2.15	2.273333333
BIN67_CONTROL_rep1_merged_R1.fastq.gz	102,966,303	2.39	2.2	2.19	2.26
BIN67_CONTROL_rep1_merged_R2.fastq.gz	102,966,303	2.4	2.2	2.33	2.31
BIN67_BRG1_rep4_merged_R1.fastq.gz	103,097,081	2.43	2.17	2.21	2.27
BIN67_BRG1_rep4_merged_R2.fastq.gz	103,097,081	2.39	2.26	2.34	2.33
Aggregate	1,484,633,500	34.7	33.35	33.33	33.79