fix #154#176
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…omes and BAM header are sorted differently
- intervals in site_bed are resorted to the order of the fragment file
- tests added to verify change works. Will fail under old behavior
- added test_wps._make_two_chrom_bam helper function to generate synthetic BAM files for test purposes
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Fix for issue where
multi_wpsoutput is missing data when BED chromosomes and BAM header are sorted differently.multi_wpsuses the header ofinput_fileif it is a BAM or CRAM file. This means it was possible to write data out of order if the order of the BED was different from the input. Previous commits improved the error handling leading toTypeError: 'NoneType' object is not iterable, however the affected chromosomes were still being dropped.site_bedare resorted to the order of the fragment filetest_wps._make_two_chrom_bamhelper function to generate synthetic BAM files for test purposes