Tests changed to reflect FastqToSam no longer fails on read if trailing /1 or /2 is missing IF the read names are identical AND don't end in /1 or /2.  Also changed test execution process to include argument parsing in CommandLineProgram.
Tests changed to reflect FastqToSam no longer fails on read if trailing /1 or /2 is missing IF the read names are identical AND don't end in /1 or /2.  Also changed test execution process to include argument parsing in CommandLineProgram.

annkupi/picard,broadinstitute/picard,nh13/picard,alecw/picard,nh13/picard,alecw/picard,annkupi/picard,broadinstitute/picard,nh13/picard,annkupi/picard,broadinstitute/picard,annkupi/picard,broadinstitute/picard,alecw/picard,nh13/picard,broadinstitute/picard,alecw/picard