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I am using your program in conjunction with the TASSEL 3 Genotyping By Sequencing Pipeline, which requires the command 'samse' to convert an .sai file to a .sam file. The example command is:
bwa samse referenceSequence/rice.fa mergedTagCounts/myAlignedMasterTags.sai mergedTagCounts/myMasterTags.cnt.fq > mergedTagCounts/myAlignedMasterTags.sam
When I use this command, windows notifies that: 'BWA.exe has stopped working - a problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available'.
So, I just wanted to check - was the program written such that the samse command is available? Any other thoughts on why this might happen? Sorry if these are really naive questions.
Thanks for your help,