freebayes does not work with low values of --min-alternate-fraction 0

[friburgo-moc]

Describe the bug

I have a bam file with ~7000 reads aligned to a reference DNA of ~500 base pairs. The majority of variants in the BAM file are present only one or two times in the total reads, so I need to use --min-alternate-fraction 0 to detect them. However, when I use this setting, the vcf file is not completed and only counts variants present until position 3 of the reference genome (and I have checked that there are more variants in the following positions)

The problem does not happen when I use a --min-alternate-fraction that is higher than 0.001 (for example 0.001, 0.01 or 0.1). However, with this setting, I obviously can not see the low-rate variants.

The problem happens only with the latest versions of freebayes. With versions lower than 1.3.0 this error does not happen.

To Reproduce

Run the following command using freebayes 1.3.0 or higher:

freebayes --pooled-continuous --min-alternate-fraction 0 --min-alternate-count 1 -f ref_seq.fasta align_sort_bamfile.bam

Edit
I have tried the command with a similar bamfile (same number of reads and same reference DNA) and it worked using freebayes 1.3.2. With freebayes versiones lower than 1.3.0 it can still work as well. The only difference is that this new bamfile has a lower number of variants.

Thanks in advance for the help!