diff --git a/clipper/fastq-mcf.cpp b/clipper/fastq-mcf.cpp
index af59e57..e508925 100644
--- a/clipper/fastq-mcf.cpp
+++ b/clipper/fastq-mcf.cpp
@@ -31,7 +31,7 @@ See "void usage" below for usage.
 
 #include "fastq-lib.h"
 
-#define VERSION "1.04.807"
+#define VERSION "1.05"
 
 #define MAX_ADAPTER_NUM 1000
 #define SCANLEN 15
@@ -174,7 +174,7 @@ class inbuffer {
                 fq->qual.s[--fq->qual.n] = '\0';
             }
  
-            return fq->qual.n > 0;
+            return fq->qual.n >= 0;  // github issue 46, 53
         } else {
             return ::read_fq(fin, rno, fq, name);
         }
@@ -220,6 +220,8 @@ int main (int argc, char **argv) {
 	int ilv3 = -1;
 	int duplen = 0;
 	int dupskip = 0;
+    int min_start_trim = 0;
+    int min_end_trim = 0;
     bool noexec = 0;
     bool hompol_filter = 0;
     bool lowcom_filter = 0;
@@ -258,6 +260,8 @@ int main (int argc, char **argv) {
        {"mate-min-len", 1, 0, 0},
        {"homopolymer-pct", 1, 0, 0},
        {"lowcomplex-pct", 1, 0, 0},
+       {"min-start-trim", 1, 0, 0},
+       {"min-end-trim", 1, 0, 0},
        {0, 0, 0, 0}
     };
 
@@ -275,6 +279,10 @@ int main (int argc, char **argv) {
                         keeponlyclip=1;
                     } else if(!strcmp(oname, "mate-qual-mean")) {
                         qf2_mean=atoi(optarg);
+                    } else if (!strcmp(oname, "min-start-trim")) {
+        		min_start_trim = atoi(optarg);
+                    } else if (!strcmp(oname, "min-end-trim")) {
+        		min_end_trim = atoi(optarg);
                     } else if(!strcmp(oname, "homopolymer-pct")) {
                         hompol_pct=atof(optarg)/100.0;
                         hompol_filter=1;
@@ -631,6 +639,10 @@ int main (int argc, char **argv) {
 				--nq; --ns;				// don't count newline for read len
 
 				// skip poor quals/lots of N's when doing sampling (otherwise you'll miss some)
+                if (ns == 0) {  // github issue 46, 53
+                    ++skipped;
+                    continue;
+                }
 				if ((st.st_size > (sampcnt * 500)) && (skipped < sampcnt) && poorqual(i, ns, s, q)) {
                     ++skipped;
 					continue;
@@ -970,6 +982,15 @@ int main (int argc, char **argv) {
 			}
 		}
 		++nrec;
+        if (fq[0].qual.n == 0) { // github issue 46, 53
+            ++nfiltered;
+            continue;
+        } else if (i_n > 1) {
+            if (fq[1].qual.n == 0) {
+                ++nfiltered;
+                continue;
+            }
+        }
 		if (read_ok < 0) {
 			++nerr;
 			continue;
@@ -1003,6 +1024,9 @@ int main (int argc, char **argv) {
 		for (f=0;f<i_n;++f) {
 			dotrim[f][0] = sktrim[f][0];					// default, trim to detected skew levels
 			dotrim[f][1] = sktrim[f][1];
+			// trim to minimum, if specified
+			dotrim[f][0] = max(dotrim[f][0], min_start_trim);
+			dotrim[f][1] = max(dotrim[f][1], min_end_trim);
 			if (avgns[f] < 11)  
 				// reads of avg length < 11 ? barcode lane, skip it
 				continue;
@@ -1493,6 +1517,10 @@ void usage(FILE *f, const char *msg) {
 "    -C N     Number of reads to use for subsampling (300k)\n"
 "    -d       Output lots of random debugging stuff\n"
 "\n"
+"Minimum trimming options:\n"
+"    --min-start-trim    NUM       Always trim at least NUM bases from start\n"
+"    --min-end-trim      NUM       Always trim at least NUM bases from end\n"
+"\n"
 "Quality adjustment options:\n"
 "    --cycle-adjust      CYC,AMT   Adjust cycle CYC (negative = offset from end) by amount AMT\n"
 "    --phred-adjust      SCORE,AMT Adjust score SCORE by amount AMT\n"
diff --git a/clipper/fastq-multx.cpp b/clipper/fastq-multx.cpp
index 0772579..6a195ec 100644
--- a/clipper/fastq-multx.cpp
+++ b/clipper/fastq-multx.cpp
@@ -34,7 +34,7 @@ See "void usage" below for usage.
 #define THFIXFACTOR 20
 #define endstr(e) (e=='e'?"end":e=='b'?"start":"n/a")
 
-const char * VERSION = "1.02.772";
+const char * VERSION = "1.03";
 
 // barcode
 struct bc {
@@ -116,6 +116,7 @@ int main (int argc, char **argv) {
 	const char* list=NULL;		// use a barcode master list
 	char verify='\0';
 	bool noexec = false;
+    bool seqnames = false;
 	const char *group = NULL;
     bool usefile1 = false;
     int phred = 33;
@@ -125,7 +126,7 @@ int main (int argc, char **argv) {
 	int i;
 	bool omode = false;	
 	char *bfil = NULL;
-	while (	(c = getopt (argc, argv, "-DzxnHhbeov:m:B:g:L:l:G:q:d:t:")) != -1) {
+	while (	(c = getopt (argc, argv, "-DzxnHhbeosv:m:B:g:L:l:G:q:d:t:")) != -1) {
 		switch (c) t:{
 		case '\1': 
                        	if (omode) {
@@ -143,6 +144,7 @@ int main (int argc, char **argv) {
 			}
 			break;
                 case 'o': omode=true; break;
+                case 's': seqnames=true; break;
                 case 'v': 
 			if (strlen(optarg)>1) {
 				fprintf(stderr, "Option -v requires a single character argument");
@@ -801,6 +803,13 @@ int main (int argc, char **argv) {
 	// TODO: output barcode read ...but only for unmatched?
 	int b;
     for (b=0;b<=bcnt;++b) {
+		size_t nameseq_len = strlen(bc[b].id.s);
+		if ((b < bcnt) && seqnames) {
+                  nameseq_len = strlen(bc[b].seq.s);
+                  if (bc[b].dual)
+                    nameseq_len += bc[b].dual_n + 1;
+		}
+
 		for (i=0;i<f_n;++i) {
 			if (!strcasecmp(out[i],"n/a") || !strcasecmp(out[i],"/dev/null")) {
 				bc[b].out[i] = NULL;
@@ -808,11 +817,20 @@ int main (int argc, char **argv) {
 				continue;
 			}
 			const char *p=strchr(out[i],'%');
-			if (!p) fail("Each output file name must contain a '%%' sign, which is replaced by the barcode id\n");
-			bc[b].out[i]=(char *) malloc(strlen(out[i])+strlen(bc[b].id.s)+100);
+			if (!p) fail("Each output file name must contain a '%%' sign, which is replaced by the barcode id or sequence\n");
+			bc[b].out[i]=(char *) malloc(strlen(out[i])+nameseq_len+100);
 			strncpy(bc[b].out[i], out[i], p-out[i]);
 			bc[b].out[i][p-out[i]]='\0';
-			strcat(bc[b].out[i], bc[b].id.s);
+			if (seqnames && (b < bcnt)) {
+			  strcat(bc[b].out[i], bc[b].seq.s);
+                          if (bc[b].dual) {
+                            strcat(bc[b].out[i], "-");
+                            strcat(bc[b].out[i], bc[b].dual);
+                          }
+                        }
+			else {
+			  strcat(bc[b].out[i], bc[b].id.s);
+                        }
 			strcat(bc[b].out[i], p+1);
 			if (!(bc[b].fout[i]=gzopen(bc[b].out[i], "w", &bc[b].gzout[i]))) {
 				fprintf(stderr, "Error opening output file '%s': %s\n",bc[b].out[i], strerror(errno));
@@ -1011,7 +1029,7 @@ int main (int argc, char **argv) {
 			if (!f) continue;
             if (!trimmed) {
 			    // todo: capture always, not just when trim is off
-                *strrchr(fq[i].id.s, '\n') = '\0';
+                if (!debug) *strrchr(fq[i].id.s, '\n') = '\0';
                 fputs(fq[i].id.s,f);
                 fputc(' ', f);
                 fputs(fq[0].seq.s,f);
@@ -1145,6 +1163,7 @@ void usage(FILE *f) {
 "-L BCFIL    Determine barcodes from <read1.fq>, using BCFIL as a master list\n"
 "-B BCFIL    Use barcodes from BCFIL, no determination step, codes in <read1.fq>\n"
 "-H          Use barcodes from illumina's header, instead of a read\n"
+"-s          Substitute barcode sequence instead of barcode label into output file names\n"
 "-b          Force beginning of line (5') for barcode matching\n"
 "-e          Force end of line (3') for batcode matching\n"
 "-t NUM      Divide threshold for auto-determine by factor NUM (1), > 1 = more sensitive\n"