0f1de4b551b0

--- a/README.markdown	Mon Feb 24 20:40:34 2020 -0500
+++ b/README.markdown	Mon Feb 24 23:56:15 2020 -0500
@@ -1006,3 +1006,10 @@
 genome but it complains that it requires the genome to be uncompressed.  Tried
 to trick it into working by psubbing `zcat` but that didn't work.  Gave up and
 decompressed the damn reference.
+
+Once the genome index was built, started aligning the reads.  It failed right
+away complaining about a zero-length read.  `zcat | grep`ing showed the read as
+being there in both files, *but* I bet this was an issue of the pairs getting
+out of sync because we grepped out the overrepresented sequences naively.  Tried
+restarting the alignment on the original data and it's still going, so that's
+probably it.  Need to figure out how to filter those bad reads properly tomorrow.