Preoprocess might fail when complex SVs are presented

[LYC-vio]

Encountered similar error mentioned in #178 when running hap.py 0.3.15 installed from Anaconda. After further debugging with

preprocess QUERY.vcf.gz:* -l chr9:42008000-42008100 -o QUERY.prep.vcf.gz -V 1 -L 1 -r REF.fa

Got the output:

[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Number=0
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Number=0
[W::bcf_hdr_register_hrec] The definition of Flag "INFO/IMPORT_FAIL" is invalid, forcing Number=0
Segmentation fault

However, when running on the vcf that only contains the variants fall in chr9:42008000-42008100 gives no errors:

chr9    42008026        .       T       C       .       .       SVTYPE=SNV;AC=1;AN=2    GT      1|0
chr9    42008079        .       T       C       .       .       SVTYPE=SNV;AC=1;AN=2    GT      1|0
chr9    42008094        .       C       T       .       .       SVTYPE=SNV;AC=1;AN=2    GT      1|0

After looking into the VCF file, found a 301319bp long INV at chr9:42009224 that might lead to the segmentation fault.

Removed all SVs in VCF and now hap.py finished without error. But still not sure whether this issue was caused by the long variant length or it was because hap.py can not handle variant types like inversions.

Hope this can help