Fix a bug which causes consensus --absent miss some absent positions

This was caused by fasta buffer being on occassions flushed too early.
It is surprisingly hard to narrow this down to a small test case
therefore, alas, no test is added with this commit

Author: pd3

NEWS

@@ -23,6 +23,8 @@ Changes affecting specific commands:
 
     - Fix a bug which prevented reading fasta files containing empty lines in their entirety (#2424)
 
+    - Fix a bug which causes `--absent` miss some absent positions
+
 * bcftools csq
 
     - Add support for complex substitutions, such as AC>TAA

consensus.c

@@ -430,7 +430,7 @@ static void flush_fa_buffer(args_t *args, int len)
 {
     if ( !args->fa_buf.l ) return;
     int nwr = 0;
-    while ( nwr + 60 <= args->fa_buf.l )
+    while ( nwr + 60 <= args->fa_buf.l && args->fa_ori_pos + nwr + 60 < args->fa_frz_pos )
     {
         if ( fwrite(args->fa_buf.s+nwr,1,60,args->fp_out) != 60 ) error("Could not write: %s\n", args->output_fname);
         if ( fwrite("\n",1,1,args->fp_out) != 1 ) error("Could not write: %s\n", args->output_fname);
@@ -462,7 +462,9 @@ static void flush_fa_buffer(args_t *args, int len)
 }
 static void apply_absent(args_t *args, hts_pos_t pos)
 {
-    if ( !args->fa_buf.l || pos <= args->fa_frz_pos + 1 || pos <= args->fa_ori_pos ) return;
+    if ( !args->fa_buf.l ) return;
+    if ( pos <= args->fa_frz_pos + 1 ) return;  // if pos==frz+1, then there is no gap, ie=ib, nothing to fill
+    if ( pos <= args->fa_ori_pos ) return;
 
     int ie = pos && pos - args->fa_ori_pos + args->fa_mod_off < args->fa_buf.l ? pos - args->fa_ori_pos + args->fa_mod_off : args->fa_buf.l;
     int ib = args->fa_frz_mod < 0 ? 0 : args->fa_frz_mod;
@@ -585,7 +587,6 @@ static int iupac_set_allele(args_t *args, bcf1_t *rec)
 static void apply_variant(args_t *args, bcf1_t *rec)
 {
     static int warned_haplotype = 0;
-
     if ( args->absent_allele ) apply_absent(args, rec->pos);
     if ( rec->n_allele==1 && !args->missing_allele && !args->absent_allele ) { return; }