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Fix vcfmerge format field handling for Number=G, INT8 PL, and dst buffer #2520

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Fix vcfmerge format field handling for Number=G, INT8 PL, and dst buffer #2520

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6 changes: 3 additions & 3 deletions vcfmerge.c
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Original file line number Diff line number Diff line change
Expand Up @@ -1653,7 +1653,7 @@ void init_local_alleles(args_t *args, bcf1_t *out, int ifmt_PL)
}
switch (fmt_ori->type)
{
case BCF_BT_INT8: BRANCH( int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, val); break;
case BCF_BT_INT8: BRANCH( int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, val>=0 && val<PL2PROB_MAX ? val : PL2PROB_MAX-1); break;
case BCF_BT_INT16: BRANCH(int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, val>=0 && val<PL2PROB_MAX ? val : PL2PROB_MAX-1); break;
case BCF_BT_INT32: BRANCH(int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, val>=0 && val<PL2PROB_MAX ? val : PL2PROB_MAX-1); break;
default: error("Unexpected case: %d, PL\n", fmt_ori->type);
Expand Down Expand Up @@ -1689,7 +1689,7 @@ void update_local_alleles(args_t *args, bcf1_t *out)
}
}
if ( j==0 ) dst[j++] = bcf_int32_missing;
for (; j<ma->nlaa; j++) src[j] = bcf_int32_vector_end;
for (; j<ma->nlaa; j++) dst[j] = bcf_int32_vector_end;
ismpl++;
}
}
Expand Down Expand Up @@ -2014,7 +2014,7 @@ void merge_localized_numberG_format_field(args_t *args, bcf_fmt_t **fmt_map, bcf
{
case BCF_BT_INT8: BRANCH(int32_t, int8_t, le_to_i8, val==bcf_int8_missing, val==bcf_int8_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
case BCF_BT_INT16: BRANCH(int32_t, int16_t, le_to_i16, val==bcf_int16_missing, val==bcf_int16_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i16, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
case BCF_BT_INT32: BRANCH(int32_t, int32_t, le_to_i32, val==bcf_int32_missing, val==bcf_int32_vector_end, tgt[tgt_idx]=bcf_int32_missing, tgt[tgt_idx]=bcf_int32_vector_end); break;
case BCF_BT_FLOAT: BRANCH(float, float, le_to_float, bcf_float_is_missing(val), bcf_float_is_vector_end(val), bcf_float_set_missing(tgt[tgt_idx]), bcf_float_set_vector_end(tgt[tgt_idx])); break;
default: error("Unexpected case: %d, %s\n", fmt_ori->type, key);
}
Expand Down