diff --git a/bwa.1 b/bwa.1
index 077dd33..d3f0458 100644
--- a/bwa.1
+++ b/bwa.1
@@ -46,7 +46,7 @@ command. It works for single-end reads only.
 .SH COMMANDS AND OPTIONS
 .TP
 .B index
-bwa index [-p prefix] [-a algoType] [-c] <in.db.fasta>
+bwa index [-p prefix] [-a algoType] <in.db.fasta>
 
 Index database sequences in the FASTA format.
 
@@ -54,7 +54,7 @@ Index database sequences in the FASTA format.
 .RS
 .TP 10
 .B -c
-Build color-space index. The input fast should be in nucleotide space.
+Build color-space index. The input fast should be in nucleotide space. (Disabled since 0.6.x)
 .TP
 .BI -p \ STR
 Prefix of the output database [same as db filename]
@@ -142,7 +142,7 @@ especially for short reads (~32bp).
 .TP
 .B -c
 Reverse query but not complement it, which is required for alignment in
-the color space.
+the color space. (Disabled since 0.6.x)
 .TP
 .B -N
 Disable iterative search. All hits with no more than
diff --git a/bwaseqio.c b/bwaseqio.c
index 600754e..90abca0 100644
--- a/bwaseqio.c
+++ b/bwaseqio.c
@@ -73,16 +73,14 @@ void seq_reverse(int len, ubyte_t *seq, int is_comp)
 
 int bwa_trim_read(int trim_qual, bwa_seq_t *p)
 {
-	int s = 0, l, max = 0, max_l = p->len - 1;
+	int s = 0, l, max = 0, max_l = p->len;
 	if (trim_qual < 1 || p->qual == 0) return 0;
 	for (l = p->len - 1; l >= BWA_MIN_RDLEN - 1; --l) {
 		s += trim_qual - (p->qual[l] - 33);
 		if (s < 0) break;
-		if (s > max) {
-			max = s; max_l = l;
-		}
+		if (s > max) max = s, max_l = l;
 	}
-	p->clip_len = p->len = max_l + 1;
+	p->clip_len = p->len = max_l;
 	return p->full_len - p->len;
 }
 
diff --git a/bwtaln.c b/bwtaln.c
index cb7cd71..18fa636 100644
--- a/bwtaln.c
+++ b/bwtaln.c
@@ -283,7 +283,7 @@ int bwa_aln(int argc, char *argv[])
 		fprintf(stderr, "         -q INT    quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
         fprintf(stderr, "         -f FILE   file to write output to instead of stdout\n");
 		fprintf(stderr, "         -B INT    length of barcode\n");
-		fprintf(stderr, "         -c        input sequences are in the color space\n");
+//		fprintf(stderr, "         -c        input sequences are in the color space\n");
 		fprintf(stderr, "         -L        log-scaled gap penalty for long deletions\n");
 		fprintf(stderr, "         -N        non-iterative mode: search for all n-difference hits (slooow)\n");
 		fprintf(stderr, "         -I        the input is in the Illumina 1.3+ FASTQ-like format\n");
diff --git a/bwtindex.c b/bwtindex.c
index 8d40245..a7b126e 100644
--- a/bwtindex.c
+++ b/bwtindex.c
@@ -65,7 +65,8 @@ int bwa_index(int argc, char *argv[])
 		fprintf(stderr, "Usage:   bwa index [-a bwtsw|div|is] [-c] <in.fasta>\n\n");
 		fprintf(stderr, "Options: -a STR    BWT construction algorithm: bwtsw or is [is]\n");
 		fprintf(stderr, "         -p STR    prefix of the index [same as fasta name]\n");
-		fprintf(stderr, "         -c        build color-space index\n\n");
+//		fprintf(stderr, "         -c        build color-space index\n");
+		fprintf(stderr, "\n");
 		fprintf(stderr,	"Warning: `-a bwtsw' does not work for short genomes, while `-a is' and\n");
 		fprintf(stderr, "         `-a div' do not work not for long genomes. Please choose `-a'\n");
 		fprintf(stderr, "         according to the length of the genome.\n\n");