From 79a2317629cce180e69662f34cee5cd1448f950e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 23 Jun 2016 08:59:42 +0100
Subject: [PATCH] mpileup: enable `-g` short `--gvcf` option that was missed

---
 mpileup.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mpileup.c b/mpileup.c
index 68c7d1ff8..057ba42cf 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -911,7 +911,7 @@ int bam_mpileup(int argc, char *argv[])
         {"open-prob", required_argument, NULL, 4},
         {"ignore-RG", no_argument, NULL, 5},
         {"ignore-rg", no_argument, NULL, 5},
-        {"gvcf", required_argument, NULL, 7},
+        {"gvcf", required_argument, NULL, 'g'},
         {"no-version", no_argument, NULL, 8},
         {"threads",required_argument,NULL,9},
         {"illumina1.3+", no_argument, NULL, '6'},
@@ -965,7 +965,7 @@ int bam_mpileup(int argc, char *argv[])
         case  3 : mplp.output_fname = optarg; break;
         case  4 : mplp.openQ = atoi(optarg); break;
         case  5 : mplp.flag |= MPLP_IGNORE_RG; break;
-        case  7 :
+        case 'g':
             mplp.gvcf = gvcf_init(optarg);
             if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
             break;