Improved warning messages in rsem-gen-transcript-plots

diff --git a/SamParser.h b/SamParser.h
index c5a503554b8c9cf4716b722d47da5f8c5db8540c..9d62eff0402ba2eca240b686b598ea3b36324ea4 100644 (file)
--- a/SamParser.h
+++ b/SamParser.h
@@ -112,8 +112,7 @@ int SamParser::parseNext(SingleRead& read, SingleHit& hit) {
        bool canR = (samread(sam_in, b) >= 0);
        if (!canR) return -1;
 
-       if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-       //(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+       general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
        int readType = getReadType(b);
        std::string name = getName(b);
@@ -143,8 +142,7 @@ int SamParser::parseNext(SingleReadQ& read, SingleHit& hit) {
        bool canR = (samread(sam_in, b) >= 0);
        if (!canR) return -1;
 
-       if (b->core.flag & 0x0001) { fprintf(stderr, "Find a paired end read in the file!\n"); exit(-1); }
-       //assert(!(b->core.flag & 0x0001)); //(b->core.flag & 0x0100) &&  && !(b->core.flag & 0x0004)
+       general_assert(!(b->core.flag & 0x0001), "Find a paired end read in the file!");
 
        int readType = getReadType(b);
        std::string name = getName(b);
@@ -175,11 +173,8 @@ int SamParser::parseNext(PairedEndRead& read, PairedEndHit& hit) {
        bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
        if (!canR) return -1;
 
-       if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-               fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-               exit(-1);
-       }
-       //assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+       general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+                       "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
        bam1_t *mp1 = NULL, *mp2 = NULL;
 
@@ -226,11 +221,8 @@ int SamParser::parseNext(PairedEndReadQ& read, PairedEndHit& hit) {
        bool canR = ((samread(sam_in, b) >= 0) && (samread(sam_in, b2) >= 0));
        if (!canR) return -1;
 
-       if (!((b->core.flag & 0x0001) && (b2->core.flag & 0x0001))) {
-               fprintf(stderr, "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)\n");
-               exit(-1);
-       }
-       //assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001));
+       general_assert((b->core.flag & 0x0001) && (b2->core.flag & 0x0001), \
+                       "One of the mate is not paired-end! (RSEM assumes the two mates of a paired-end read should be adjacent)");
 
        bam1_t *mp1 = NULL, *mp2 = NULL;
 

diff --git a/rsem-gen-transcript-plots b/rsem-gen-transcript-plots
index 9a806d6c191710482b896105c3e965a49828af3e..21d1db829174ca56e3c25a3f1afe59085db492af 100755 (executable)
--- a/rsem-gen-transcript-plots
+++ b/rsem-gen-transcript-plots
@@ -67,7 +67,7 @@ generate_a_page <- function(tids, gene_id = NULL) {
 
   for (i in 1:n) {
     vec <- readdepth[[tids[i]]]
-    if (is.null(vec)) exit_with_error(paste("Cannot find transcript", tids[i], sep = ""))
+    if (is.null(vec)) exit_with_error(paste("Unknown transcript detected,", tids[i], "is not included in RSEM's indices."))
     if (is.na(vec[[2]])) wiggle <- rep(0, vec[[1]]) else wiggle <- as.numeric(unlist(strsplit(vec[[2]], split = " ")))
     len <- length(wiggle)
     if (!show_uniq) {
@@ -113,7 +113,7 @@ if (!is_gene) {
   }
 } else {
   for (gene_id in ids) {
-    if (is.null(t2gmap[[gene_id]])) exit_with_error(paste("Cannot find gene", gene_id, sep = ""))
+    if (is.null(t2gmap[[gene_id]])) exit_with_error(paste("Unknown gene detected,", gene_id, "is not included in RSEM's in indices."))
     generate_a_page(t2gmap[[gene_id]], gene_id)
   }
 }
@@ -121,9 +121,3 @@ if (!is_gene) {
 cat("Plots are generated!\n)
 
 dev.off.output <- dev.off()
-
-
-
-
-
-