# HG changeset patch # User Steve Losh # Date 1774298642 14400 # Node ID 47647c58a95959c591a0c376175775985304d158 # Parent 02081983e4e7b0e36cd86a39e661cb758318d135 Fixup README diff -r 02081983e4e7 -r 47647c58a959 README.markdown --- a/README.markdown Mon Mar 23 16:41:36 2026 -0400 +++ b/README.markdown Mon Mar 23 16:44:02 2026 -0400 @@ -56,16 +56,17 @@ ((x 100)) #(x 500 x) -Generate a foldback chimeric read, with the second half having a lower quality -than the first: +Generate a gapped foldback chimeric read, with the second half having a lower +quality than the first: - ((x (q40 1000))) - #(x (q20 (revcomp x))) + ((x (q40 1000)) + (f (q20 (revcomp x)))) + #(x 25 f) Generate a read with a tandem repeat in the middle: () - (1000 (rep 200 "ATTT")) + (1000 (rep 200 "ATTT") 1000) Generate a foldback chimeric read with a double tandem duplication in the foldback strand, with simulated sequencing error, and small chunks of @@ -76,6 +77,6 @@ (a (first 800 x)) (b (last 200 x)) (dup (last 150 a)) - (f #(lq a lq dup lq (rc dup) lq dup lq b))) + (f (revcomp #(lq a lq dup lq (rc dup) lq dup lq b)))) - (err 0.01 #(x (revcomp f))) + (err 0.01 #(x f))