It appears that -A still prints "Program" in the stats log file about htstream

[samhunter]

Okay, that totally didn't work:

Program TotalRecords R2_Discarded R1_Discarded R2_Length SE_Out SE_Length Ignored TotalReadsInput PE_In PE_Out SE_In SE_Left_Trim Sins Replaced SE_Discarded R2_Right_Trim R1_Left_Trim SE_Right_Trim R1_Right_Trim R1_Length R2_Left_Trim Overlap_BPs Lins

Super-Deduper 267139 0 0 66367161 0 0 0 0 0 264411 0 0 0 2728 0 0 0 0 0 66367161 0 0 0

Program Q-Trim 264411 14 0 65862254 14 0 0 0 0 264397 0 0 0 0 0 496200 231 0 440264 65926666 5193 0 0

Program Overlapper 264411 0 0 24600101 163746 41630620 0 0 0 98694 0 0 0 0 1971 0 0 0 0 24669593 0 0 0

[msettles]

I'm not sure I like this stats output format, for one I can't tell what some of these actually mean, I get that you need something that will append as you go, but seems to leave out a lot of stats that are sub-app specific, and doesn't really allow for the flexibility of new apps (new stats) etc. Nor does it offer an easy way to summarize and then compare across samples. SO might I suggest a json formatted output, that can then be read into a post processing app (in R maybe) and certain keys can be picked up and summarized. One of the huge advantages in HTStream is that others can create apps that can also go into the stream, but abiding by a stats table may limit their usefulness, a json formatted file will then offer that flexibility.

[msettles]

no longer relevant