test.sh

#!/usr/bin/env bash

BASH_TAP_ROOT=bash-tap
source ./bash-tap/bash-tap-bootstrap

PATH=../bin:$PATH # for freebayes

plan tests 1

ref=$(basename $0).ref
bam=$(basename $0).bam

trap 'rm -f ${ref}* ${bam}*' EXIT

function make_ref() {
    local bases=$1 && shift
    cat >${ref} <<REF
>ref
${bases}
REF
    samtools faidx ${ref}
}

samtools view -S -b - >${bam} <<SAM
@HD VN:1.5	SO:coordinate
@SQ	SN:ref	LN:19
alt	0	ref	1	30	1=1X1=12X1=1X1=1X	*	0	0	AGTTAAAAAAAAAAAGGTT	*
SAM
samtools index ${bam}

function run_freebayes() {
    freebayes --haplotype-length 0 --min-alternate-count 1 \
              --min-alternate-fraction 0 --pooled-continuous --report-monomorphic \
              --ploidy 1 \
              -f $ref $bam \
              2>&1 \
        | grep -vE "^#" | cut -f1-5
}

expected=$(cat <<END
ref	2	.	A	G
ref	4	.	CNNNNNNNNNNN	TAAAAAAAAAAA
ref	17	.	C	G
ref	19	.	A	T
END
)
make_ref "AATCNNNNNNNNNNNGCTA"
is "$(run_freebayes)" "${expected}" "freebayes calls after long haplotype"