Fix handling of skipped lines in bcftools norm -c x
#2436
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Make normalize_line() report when it skips a line due to a ref mismatch so that normalize_vcf() knows that it has to go on to the next one. Failing to do this caused a crash when the first input line was skipped because normalize_vcf() attempted to access data via args->rbuf when nothing had been added. The input file for the `bcftools norm -c x` did not catch this because the line it skipped was towards the end of the file. An extra record has been added at the front, which does trigger the issue on the original code.
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Make
normalize_line()report when it skips a line due to a ref mismatch so thatnormalize_vcf()knows that it has to go on to the next one.Failing to do this caused a crash when the first input line was skipped because
normalize_vcf()attempted to access data via args->rbuf when nothing had been added.The input file for the
bcftools norm -c xdid not catch this because the line it skipped was towards the end of the file. An extra record has been added at the front, which does trigger the issue on the original code.Fixes #2427