Pointing gramtools at current SDSL results in assertion failure in unit tests about gramtools HOT 7 CLOSED

FFS I can't reproduce it!!

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Ah yes, now I can after make clean. This time used printf
right=0 and left=25

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Adding a print to see what each c is (c=*pat_it)

[ RUN ] BackwardSearchTest.OneSNP
PRG size: 27
Alphabet size: 5
c is 3
c is 1
c is 3
c is 1
c is 3
c is 1
c is 4
c is 2
c is 1
c is 1
c is 3
oops right is 0and left is 25
unittest_bidir_search_bwd_fwd: ./skip.cpp:116: bool skip(sdsl::csa_wtsdsl::wt_int<sdsl::int_vector<1u, sdsl::rank_support_v5<> >, 2u, 16777216u>&, uint64_t&, uint64_t&, uint64_t&, uint64_t&, uint32_t): Assertion `right>left' failed.

OK, so what does this mean.
The read is:
ttacacagaactagagag

the prg is: catttacaca5g6t5aactagagagca

So it breaks on the g which is allele 1

For the record the BWM is

$catttacaca5g6t5aactagagagca
5aactagagagca$catttacaca5g6t
5g6t5aactagagagca$catttacaca
6t5aactagagagca$catttacaca5g
a$catttacaca5g6t5aactagagagc
a5g6t5aactagagagca$catttacac
aactagagagca$catttacaca5g6t5
aca5g6t5aactagagagca$catttac
acaca5g6t5aactagagagca$cattt
actagagagca$catttacaca5g6t5a
agagagca$catttacaca5g6t5aact
agagca$catttacaca5g6t5aactag
agca$catttacaca5g6t5aactagag
atttacaca5g6t5aactagagagca$c
ca$catttacaca5g6t5aactagagag
ca5g6t5aactagagagca$catttaca
caca5g6t5aactagagagca$cattta
catttacaca5g6t5aactagagagca$
ctagagagca$catttacaca5g6t5aa
g6t5aactagagagca$catttacaca5
gagagca$catttacaca5g6t5aacta
gagca$catttacaca5g6t5aactaga
gca$catttacaca5g6t5aactagaga
t5aactagagagca$catttacaca5g6
tacaca5g6t5aactagagagca$catt
tagagagca$catttacaca5g6t5aac
ttacaca5g6t5aactagagagca$cat <<< index 25
tttacaca5g6t5aactagagagca$ca

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This BWM is wrong. Why are the rows starting with 5 before the rows starting with a when a is 1 in integer alphabet?

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yes, is wrong, made this when I had a bug in my script for printing BWM. Will fix

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BWM is
$214441212153645112413131321
1$21444121215364511241313132
112413131321$214441212153645
1212153645112413131321$21444
12153645112413131321$2144412
12413131321$2144412121536451
13131321$2144412121536451124
131321$214441212153645112413
1321$21444121215364511241313
14441212153645112413131321$2
153645112413131321$214441212
21$2144412121536451124131313
212153645112413131321$214441
214441212153645112413131321$
2153645112413131321$21444121
2413131321$21444121215364511
3131321$21444121215364511241
31321$2144412121536451124131
321$214441212153645112413131
3645112413131321$21444121215
41212153645112413131321$2144
413131321$214441212153645112
441212153645112413131321$214
4441212153645112413131321$21
45112413131321$2144412121536
5112413131321$21444121215364
53645112413131321$2144412121
645112413131321$214441212153

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Can we close this @rffrancon

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