Add warning messages for detected invalid alignments

diff --git a/PairedEndModel.h b/PairedEndModel.h
index 70d14c9de9a97680eb9a683715f887a1d2a1e16f..575344c348c6aa1783b66e98a3d760484ec27e22 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -10,6 +10,7 @@
 #include<sstream>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -99,7 +100,15 @@ public:
                int fpos = (dir == 0 ? pos : totLen - pos - insertLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
                int effL = std::min(fullLen, totLen - insertLen + 1);
                
-               assert(fpos >= 0 && fpos + insertLen <= totLen && insertLen <= totLen);
+               general_assert(fpos >= 0, "The alignment of fragment " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+                               " from the forward direction, which should be a non-negative number! " + \
+                               "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(fpos + insertLen <= totLen,"Fragment " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+                               + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(insertLen <= totLen, "Fragment " + read.getName() + " has length " + itos(insertLen) + ", but it is aligned to transcript " \
+                               + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the fragment's length!");
+
+
                if (fpos >= fullLen || ref.getMask(fpos)) return 0.0; // For paired-end model, fpos is the seedPos
 
                prob = ori->getProb(dir) * gld->getAdjustedProb(insertLen, totLen) *

diff --git a/PairedEndQModel.h b/PairedEndQModel.h
index 2c638abed103bcf4f7167b70b60221aa9eafed88..c61f6c872eaa26be6db47eac88de2c174a1c634f 100644 (file)
--- a/PairedEndQModel.h
+++ b/PairedEndQModel.h
@@ -10,6 +10,7 @@
 #include<sstream>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -103,7 +104,14 @@ public:
                int fpos = (dir == 0 ? pos : totLen - pos - insertLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
                int effL = std::min(fullLen, totLen - insertLen + 1);
 
-               assert(fpos >= 0 && fpos + insertLen <= totLen && insertLen <= totLen);
+               general_assert(fpos >= 0, "The alignment of fragment " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+                               " from the forward direction, which should be a non-negative number! " + \
+                               "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(fpos + insertLen <= totLen,"Fragment " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+                               + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(insertLen <= totLen, "Fragment " + read.getName() + " has length " + itos(insertLen) + ", but it is aligned to transcript " \
+                               + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the fragment's length!");
+
                if (fpos >= fullLen || ref.getMask(fpos)) return 0.0; // For paired-end model, fpos is the seedPos
 
                prob = ori->getProb(dir) * gld->getAdjustedProb(insertLen, totLen) *

diff --git a/SingleModel.h b/SingleModel.h
index 59db6ec69d30ce228535312f9cd91da476be2cae..8b26e0e36dd4e919eb5635d2504617a9c7b841ca 100644 (file)
--- a/SingleModel.h
+++ b/SingleModel.h
@@ -10,6 +10,7 @@
 #include<sstream>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -102,7 +103,14 @@ public:
                int readLen = read.getReadLength();
                int fpos = (dir == 0 ? pos : totLen - pos - readLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
 
-               assert(fpos >= 0 && fpos + readLen <= totLen && readLen <= totLen);
+               general_assert(fpos >= 0, "The alignment of read " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+                               " from the forward direction, which should be a non-negative number! " + \
+                               "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(fpos + readLen <= totLen,"Read " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+                               + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(readLen <= totLen, "Read " + read.getName() + " has length " + itos(readLen) + ", but it is aligned to transcript " \
+                               + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the read's length!");
+
                int seedPos = (dir == 0 ? pos : totLen - pos - seedLen); // the aligned position of the seed in forward strand coordinates
                if (seedPos >= fullLen || ref.getMask(seedPos)) return 0.0;
 

diff --git a/SingleQModel.h b/SingleQModel.h
index 786d6476383ec41fb06606f74c49099786f693e7..ffc0639909b2f49a5d501c7ecb85be20f2f19f4f 100644 (file)
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -10,6 +10,7 @@
 #include<sstream>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -108,7 +109,14 @@ public:
                int readLen = read.getReadLength();
                int fpos = (dir == 0 ? pos : totLen - pos - readLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
 
-               assert(fpos >= 0 && fpos + readLen <= totLen && readLen <= totLen);
+               general_assert(fpos >= 0, "The alignment of read " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+                               " from the forward direction, which should be a non-negative number! " + \
+                               "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(fpos + readLen <= totLen,"Read " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+                               + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(readLen <= totLen, "Read " + read.getName() + " has length " + itos(readLen) + ", but it is aligned to transcript " \
+                               + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the read's length!");
+
                int seedPos = (dir == 0 ? pos : totLen - pos - seedLen); // the aligned position of the seed in forward strand coordinates
                if (seedPos >= fullLen || ref.getMask(seedPos)) return 0.0;