Make -d, --max-depth 0 set the depth to unlimited

This is to behave the same way as `samtools mpileup`

Resolves #2435

Author: pd3

NEWS

@@ -26,6 +26,10 @@ Changes affecting specific commands:
     - Fix an error in parsing -i/-e command line options where the `qry:` and `gt:` prefix was
       not stripped (#2432)
 
+* bcftools mpileup
+
+    - Make `-d, --max-depth 0` set the depth to unlimited (#2435)
+
 * bcftools norm
 
     - Make the -i/-e filtering option work for all options, such as line merging and

doc/bcftools.txt

@@ -2308,7 +2308,8 @@ those scenarios.
     This behavior was problematic when working with a combination of
     single- and multi-sample bams, therefore in *bcftools mpileup* the user
     is given the full control (and responsibility), and an informative message
-    is printed instead [250]
+    is printed instead. Passing zero for this option sets it to the highest possible
+    value, effectively removing the depth limit [250]
 
 *-E, --redo-BAQ*::
     Recalculate BAQ on the fly, ignore existing BQ tags

mpileup.c

@@ -930,11 +930,19 @@ static int mpileup(mplp_conf_t *conf)
     // init mpileup
     conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data);
     if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter);
-    fprintf(stderr, "[%s] maximum number of reads per input file set to -d %d\n",  __func__, conf->max_depth);
-    if ( (double)conf->max_depth * conf->nfiles > 1<<20)
-        fprintf(stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles);
-    if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 )
-        fprintf(stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl);
+    if ( !conf->max_depth )
+    {
+        conf->max_depth = INT_MAX;
+        fprintf(stderr, "[%s] Max depth set to maximum value (%d)\n", __func__, INT_MAX);
+    }
+    else
+    {
+        fprintf(stderr, "[%s] maximum number of reads per input file set to -d %d\n",  __func__, conf->max_depth);
+        if ( (double)conf->max_depth * conf->nfiles > 1<<20)
+            fprintf(stderr, "Warning: Potential memory hog, up to %.0fM reads in the pileup!\n", (double)conf->max_depth*conf->nfiles);
+        if ( (double)conf->max_depth * conf->nfiles / nsmpl < 250 )
+            fprintf(stderr, "Note: The maximum per-sample depth with -d %d is %.1fx\n", conf->max_depth,(double)conf->max_depth * conf->nfiles / nsmpl);
+    }
     bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
     conf->max_indel_depth = conf->max_indel_depth * nsmpl;
     conf->bcf_rec = bcf_init1();