I'm using bfast 0.7.0a and testing on the paired end data present in the bfast user manual (Figure 5.4 in bfast-book.pdf). The format for this fastq file is shown that paired reads should follow sequentially in the file (read1*R1, read1*R2, read2*R1, read2*R2, etc). The same name is to be used for the sequential reads in a pair. So, the user manual data has 4 reads = two pairs. When I run bfast match:

bfast match -A 0 -t -n 16 -f hg19.fa -i 1 -r bfast_book.fastq
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName hg19.fa.
Validating readsFileName bfast_book.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode:                            [ExecuteProgram]
fastaFileName:                          hg19.fa
mainIndexes                             1
secondaryIndexes                        [Not Using]
readsFileName:                          bfast_book.fastq
offsets:                                [Using All]
loadAllIndexes:                         [Not Using]
compression:                            [Not Using]
space:                                  [NT Space]
startReadNum:                           1
endReadNum:                             2147483647
keySize:                                [Not Using]
maxKeyMatches:                          8
keyMissFraction:                        1.000000
maxNumMatches:                          384
whichStrand:                            [Both Strands]
numThreads:                             16
queueLength:                            250000
tmpDir:                                 ./
timing:                                 [Using]
************************************************************
Searching for main indexes...
Found 1 index (1 file).
Not using secondary indexes.
************************************************************
Reading in reference genome from hg19.fa.nt.brg.
In total read 85 contigs for a total of 3101810128 bases
************************************************************
Reading bfast_book.fastq into a temp file.
Will process 2 reads.
************************************************************
Searching index file 1/1 (index #1, bin #1)...

There are four reads in this file; why does it say that it will process two reads? I've tested this on my own data as well. I just want to make sure that it is really aligning all four reads (as far as I could tell, bfast match is not paired-read aware; that comes in the postprocess step).

Thank you!