python /home2/georgi/code/filterSAMSplices.py accepted_hits.sam accepted_hits.splices.sam
/woldlab/rattus/lvol0/mus/proj/genome/programs/samtools-0.1.7a/samtools view -bT ~/genomes/hg19/male.hg19.fa accepted_hits.splices.sam -o accepted_hits.splices.bam
/woldlab/rattus/lvol0/mus/proj/genome/programs/samtools-0.1.7a/samtools index accepted_hits.splices.bam 
/woldlab/castor/data00/proj/genome/programs/x86_64/validateFiles-1.42 -type=BAM -maxErrors=100000000 -genome=/woldlab/castor/data00/home/georgi/genomes/hg19/male.hg19.2bit -chromInfo=/woldlab/castor/data00/home/georgi/genomes/hg19/male.hg19.chrom.sizes -mismatches=6 accepted_hits.splices.bam -verbose=2