Replace GNU parallel with tee

[njspix]

I recently ran into a bug using a new version of GNU parallel. I quickly developed a bit of annoyance when I had a difficult time finding a changelog for parallel. I believe the 'tee' command should work just as well and it's a lot easier to read.

(edit) OK, maybe it's not as easy to read anymore... :-D

[njspix]

Tests on sample bam files:

tee, single cell

• real 2m52.947s
• user 2m30.063s
• sys 0m28.862s

parallel, single cell

• real 2m51.425s
• user 5m41.463s
• sys 0m32.889s

tee, bulk

• real 61m50.013s
• user 95m12.041s
• sys 26m16.641s

parallel, bulk

• real 61m30.633s
• user 100m6.832s
• sys 26m19.267s

files produced are identical by md5sum

[njspix]

Updated with more/hopefully better comments clarifying how the tee code works

[njspix]

Just gave this a test run on a medium-sized BAM. Results below:

Finished BISCUIT QC at Tue Sep 27 10:24:41 EDT 2022
real	17m29.583s
user	47m22.398s
sys	5m16.096s

Finished BISCUIT QC at Tue Sep 27 10:42:04 EDT 2022
real	17m23.558s
user	46m36.619s
sys	5m15.435s

00ef368e28bc23c9d8e011e882cbe108  parallel_CpHRetentionByReadPos.txt
00ef368e28bc23c9d8e011e882cbe108  tee_CpHRetentionByReadPos.txt
05d330834eee785d10cb08bc92450d08  parallel_covdist_all_cpg_topgc_table.txt
05d330834eee785d10cb08bc92450d08  tee_covdist_all_cpg_topgc_table.txt
0d01f101ae0558f120612441847497d1  parallel_cv_table.txt
0d01f101ae0558f120612441847497d1  tee_cv_table.txt
21f36255266994f59e2065ecdc46ee35  parallel_CpGRetentionByReadPos.txt
21f36255266994f59e2065ecdc46ee35  tee_CpGRetentionByReadPos.txt
347e8979a45698944a8b84004327cefd  parallel_covdist_q40_base_topgc_table.txt
347e8979a45698944a8b84004327cefd  tee_covdist_q40_base_topgc_table.txt
421094667ca7675b69817709e26f332c  parallel_isize_table.txt
421094667ca7675b69817709e26f332c  tee_isize_table.txt
4d05292b54d2b30eefe36fbea4758478  parallel_totalReadConversionRate.txt
4d05292b54d2b30eefe36fbea4758478  tee_totalReadConversionRate.txt
4dcfe62f7a1b117d61e34f21eec79669  parallel_mapq_table.txt
4dcfe62f7a1b117d61e34f21eec79669  tee_mapq_table.txt
50d439ecdbce24e1d4293aeedb66c3ba  parallel_covdist_all_base_table.txt
50d439ecdbce24e1d4293aeedb66c3ba  tee_covdist_all_base_table.txt
89880ce1c6b67699f7b106d92f1e0d42  parallel_covdist_q40_base_table.txt
89880ce1c6b67699f7b106d92f1e0d42  tee_covdist_q40_base_table.txt
8cd0fb99738cd394f9159775e6042ab1  parallel_covdist_all_base_botgc_table.txt
8cd0fb99738cd394f9159775e6042ab1  tee_covdist_all_base_botgc_table.txt
a7cf43fc5f0f8043d288a7503146ccef  parallel_dup_report.txt
a7cf43fc5f0f8043d288a7503146ccef  tee_dup_report.txt
aaceddf2f79fd55ca71d99ceb6dc78d7  parallel_covdist_q40_cpg_topgc_table.txt
aaceddf2f79fd55ca71d99ceb6dc78d7  tee_covdist_q40_cpg_topgc_table.txt
ac36d069cd44425c2fb26a464ae81472  parallel_covdist_q40_base_botgc_table.txt
ac36d069cd44425c2fb26a464ae81472  tee_covdist_q40_base_botgc_table.txt
b3ab4899c23d4b6db83f0fddc513ab09  parallel_covdist_all_cpg_table.txt
b3ab4899c23d4b6db83f0fddc513ab09  tee_covdist_all_cpg_table.txt
b5cde1b72db50677574903a5174f4fab  parallel_covdist_q40_cpg_botgc_table.txt
b5cde1b72db50677574903a5174f4fab  tee_covdist_q40_cpg_botgc_table.txt
be38874b9b518e08e89502bfa071dafd  parallel_strand_table.txt
be38874b9b518e08e89502bfa071dafd  tee_strand_table.txt
d9e8ba48fb2af5fff06dd25092f2eee2  parallel_covdist_all_base_topgc_table.txt
d9e8ba48fb2af5fff06dd25092f2eee2  tee_covdist_all_base_topgc_table.txt
f2f473fdb9e52ee0e590ad9a47c2afb1  parallel_covdist_q40_cpg_table.txt
f2f473fdb9e52ee0e590ad9a47c2afb1  tee_covdist_q40_cpg_table.txt
f4126f00d2ea0ef8c5b8eb65d06d4aad  parallel_covdist_all_cpg_botgc_table.txt
f4126f00d2ea0ef8c5b8eb65d06d4aad  tee_covdist_all_cpg_botgc_table.txt

[jamorrison]

This has been resolved with PR #31 and superseded by PR #33.