segmentation fault

[RamilNurtdinov]

Hi
I am getting the error below. I made small reproducible example and attached it "split.txt". 64bit version of the program

---

$ gt readjoiner prefilter -db split.txt
# gt readjoiner prefilter (version 1.2)
# number of reads in complete readset = 14
# low-quality reads = 0
# contained reads = 1
# number of reads in filtered readset = 13
Assertion failed: ((code & ~mask) >> shift == (GtTwobitencoding)r2t->current_sepcode), function gt_reads2twobit_set_separators_to_less_frequent_char, file src/match/reads2twobit.c, line 1976.
This is a bug, please report it at

gt -version
gt (GenomeTools) 1.6.1
Copyright (c) 2003-2016 G. Gremme, S. Steinbiss, S. Kurtz, and CONTRIBUTORS
Copyright (c) 2003-2016 Center for Bioinformatics, University of Hamburg
See LICENSE file or http://genometools.org/license.html for license details.

Used compiler: cc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
Compile flags:  -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -Wno-unknown-pragmas -O3 -Werror

split.txt

[satta]

I just took a brief look and it seems to be caused by sequence URS00000E9CEF being contained in URS00000EBA19. If I change the sequence to remove that containment then we don't hit this error. Also, moving URS00000EBA19 away from the end of the sequence set (so that it is not the last sequence) also fixes it.
See split2.txt.

I have a hunch that this is a corner case in the 2bit-encoding code that handles containment involving the last sequence in the input differently. Any ideas @ggonnella?