Perl Bio::DB::Sam crashes during call to get_features_by_id()

Question

I am using Bio::DB::Sam in a Centos7 environment, using version 0.1.17 of samtools. I am using this procedure to perform my installation:

wget http://sourceforge.net/projects/samtools/files/samtools/0.1.17/samtools-0.1.17.tar.bz2
tar xjf samtools-0.1.17.tar.bz2 && cd samtools-0.1.17
make CFLAGS=-fPIC
export SAMTOOLS=`pwd`
cpanm Bio::DB::Sam

which I discovered here (notice I changed the version of samtools)

The crash occurs intermittently, sometimes on the same input files. My general procedure is as follows:

1. Use bowtie to generate a .sam file from a .fastq file, using a custom bowtie index
2. Use samtools to convert my .sam to a .bam, sorting and indexing the file along the way
3. Issue the following Perl commands:

Perl:

my $sortbam = align_and_sort_and_index($reads_file);   # steps 1 and 2
my @all_gene_ids = qw(gene_id1 gene_id2 gene_id3);   # really lots more
for (my $worker=0; $worker <= $n_threads; $worker++) {
    my $pid = fork;
    die "fork error: $!" unless defined $pid;
    next if $pid;     # parent
    my @gene_ids = get_unique_subset(@all_gene_ids, $worker);
    my $sam = Bio::DB::Sam->new(-bam=>$sortbam, -fasta=>$ampl_seqfile, -autoindex=>0);
    foreach my $gene_id (@gene_ids) {
        # THIS NEXT LINE IS THE ONE THAT SEGFAULTS (SOMETIMES):
        my @alignments = $sam->get_features_by_location(-seq_id => $gene_id);
        # do something interesting with @alignments...
    }
    exit;
}

while ((my $pid=wait()) != -1) {
    print "reaped $pid\n";
}

To date I have tried the following:

1. Increased the number of allowed open files (ulimit -n)
2. Increased the number of number of allowed subprocesses
3. Increased the limit of pipe buffers
4. Increased the swap space

Any and all suggestions would be greatly appreciated. Thank you!