Errata

Probability should be ... "> $chilevels[$i+1] and..." rather than using "<" for both upper & lower probability bounds. (This seems to be an error in transcribing existing utility code for a Chi Square probability estimate.)

In the discussion of arrays:

"$array = [ [ 'Dennis', 'Draya'], ['Callum', 'Bell']]

The following are synonymous:

print $$array[1][2];
print $array->[1][2];
print $array->[1]->[2];

Here's the output:

BellBellBell"

This looks wrong to me -- as the subscript [1][2] is out of bounds. To get "Bell" as
an output would require:

print $$array[1][1]; or one of the suitable variations.

print $$array[1][2];
print $array->[1][2];
print $array->[1]->[2];

should read:

print $$array[1][1];
print $array->[1][1];
print $array->[1]->[1];

the edit distance between the two strings (portend--->profound) is 4 and not 5.

portend
insert r
prortend
change r to f
proftend
change t to o
profoend
change e to u
profound

if you use the example-script on page 62 with:
my $pattern = 'portend';
my $text = 'profound';
you also get the edit distance 4.

In the following code rows and columns are reversed:

# The rows correspond to the text
# Initialize row 0 of D.
for (my $t=0; $t <= $TLEN ; ++$t) {
$D->[$t][0] = 0;
}

# The columns correspond to the pattern
# Initialize column 0 of D.
for (my $p=0; $p <= $PLEN ; ++$p) {
$D->[0][$p] = $p;
}

In a 2 dimensional array, classically, the row comes first, as in $array[row][col];

The print of the array works because there is a similar reversal in the print
statement for the array.

The expressions "row" and "column" should be interchanged. As it reads, "row $t"
corresponds to a "substring of the text ending at text position $t". As depicted,
the number of rows is equal to the size of the pattern, not the size of the text.

the CREATE TABLE statements are in error. The tables are named in
lower case (i.e., "organism" instead of "ORGANISM"), preventing the code (in
homologs.tabs) from testing exactly as shown on page 229
(result is:
genes
organism
variants

instead of
GENES
ORGANISM
VARIANTS)

This also causes the homologs.load (pp. 231-232) to fail when attempting to insert
data from homologs.tabs (typed as shown on page 226) into, for example, a table named
"genes" instead of GENES, "geneid" instead of GeneId, etc.

Dropping the homologs database and recreating using upper case table names (and
initial cap field names, etc.) allows the data to be correctly inserted into the
MySQL database and results in the output shown on the bottom of page 232.