The following is a brief summary of how to run the crossmatch to SAM converter tool:

ALLXMATCH.chr1 is the input crossmatch file example

reads.chr1.fa.0.gz is the input read sequence file, zipped

reads.chr1.fa.qual.0.gz is the input read quality file, zipped

chr1 is the reference sequence file

example command is "ruby crossmatch2SAM_v1.1.rb -i ALLXMATCH.chr1 -o ALLXMATCH.chr1.sam -r reads.chr1.fa.0.gz -q reads.chr1.fa.qual.0.gz -f chr1"

ALLXMATCH.chr1.sam is the output SAM file

For users who want to convert SAM file to BAM format, samtools should be
installed first. Then use command "samtools import reference_list_file
sam_file bam_file".

For any question or commend, please contact me at yw14@bcm.tmc.edu. Thank you
very much for using this tool, any suggestion will be appreciated!