Fix bed_index_core() handling of overlapping entries#2107
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It needs to skip if the current entry ends before the previous one, which can happen if the input BED file has entries that are completely contained in an earlier region. Failing to do this could cause last_end to jump backwards, resulting in some incorrect entries being put in the index. This could lead to hits between the end of the innermost and outermost nested BED entries being missed. Fixes samtools#2104 ("samtools view -L " incomplete output for BED with nested targets)
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It needs to skip if the current entry ends before the previous one, which can happen if the input BED file has entries that are completely contained in an earlier region. Failing to do this could cause last_end to jump backwards, resulting in some incorrect entries being put in the index. This could lead to hits between the end of the innermost and outermost nested BED entries being missed.
Fixes #2104 ("samtools view -L " incomplete output for BED with nested targets)