[med-svn] [Git][med-team/last-align][upstream] New upstream version 1260
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed Feb 16 11:21:40 GMT 2022
Nilesh Patra pushed to branch upstream at Debian Med / last-align
Commits:
7d8889ea by Nilesh Patra at 2022-02-16T16:39:14+05:30
New upstream version 1260
- - - - -
7 changed files:
- bin/maf-cut
- src/Alphabet.hh
- src/lastal.cc
- src/makefile
- src/mcf_reverse_queue.hh
- test/last-test.out
- test/last-test.sh
Changes:
=====================================
bin/maf-cut
=====================================
@@ -31,6 +31,9 @@ def alnEndFromSeqEnd(gappedSequence, seqEnd):
return i + 1
def alignmentRange(cutBeg, cutEnd, sLineFields):
+ if sLineFields[4] == "-":
+ seqLen = int(sLineFields[5])
+ cutBeg, cutEnd = seqLen - cutEnd, seqLen - cutBeg
beg = int(sLineFields[2])
if beg >= cutEnd:
return 0, 0
=====================================
src/Alphabet.hh
=====================================
@@ -11,6 +11,8 @@
#ifndef ALPHABET_HH
#define ALPHABET_HH
+#include <stddef.h>
+
#include <string>
#include <iosfwd>
@@ -36,6 +38,14 @@ struct Alphabet{
// add counts of "proper" letters to "counts" (counting lowercase too)
void count( const uchar* beg, const uchar* end, countT* counts ) const;
+ size_t countNormalLetters(const uchar *beg, const uchar *end) const {
+ size_t c = 0;
+ for (const uchar *i = beg; i < end; ++i) {
+ c += (numbersToUppercase[*i] < size);
+ }
+ return c;
+ }
+
// translate (encode) a sequence of letters to numbers, in place
void tr( uchar* beg, uchar* end, bool isKeepLowercase=true ) const;
=====================================
src/lastal.cc
=====================================
@@ -43,10 +43,13 @@ static void warn( const char* programName, const char* s ){
using namespace cbrc;
+typedef unsigned long long countT;
+
struct LastAligner { // data that changes between queries
Aligners engines;
std::vector<int> qualityPssm;
std::vector<AlignmentText> textAlns;
+ countT numOfNormalLetters;
};
struct SubstitutionMatrices {
@@ -69,8 +72,6 @@ struct SubstitutionMatrices {
};
namespace {
- typedef unsigned long long countT;
-
LastalArguments args;
Alphabet alph;
Alphabet queryAlph; // for translated alignment
@@ -1109,6 +1110,12 @@ void translateAndScan(LastAligner &aligner, size_t finalCullingLimit,
static void alignOneQuery(LastAligner &aligner, size_t finalCullingLimit,
size_t queryNum, bool isFirstVolume) {
+ if (isFirstVolume) {
+ aligner.numOfNormalLetters +=
+ queryAlph.countNormalLetters(query.seqReader() + query.seqBeg(queryNum),
+ query.seqReader() + query.seqEnd(queryNum));
+ }
+
if (args.strand == 2 && !isFirstVolume)
query.reverseComplementOneSequence(queryNum, queryAlph.complement);
@@ -1442,7 +1449,12 @@ void lastal( int argc, char** argv ){
scanAllVolumes( volumes, out );
}
- out << "# Query sequences=" << sequenceCount << "\n";
+ countT numOfNormalLetters = 0;
+ for (size_t i = 0; i < aligners.size(); ++i) {
+ numOfNormalLetters += aligners[i].numOfNormalLetters;
+ }
+ out << "# Query sequences=" << sequenceCount
+ << " normal letters=" << numOfNormalLetters << "\n";
}
int main( int argc, char** argv )
=====================================
src/makefile
=====================================
@@ -143,7 +143,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1257) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1260) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
src/mcf_reverse_queue.hh
=====================================
@@ -32,7 +32,7 @@ public:
if (!p) throw std::bad_alloc();
end = static_cast<T *>(p) + newLen;
beg = end - numOfOldItemsToKeep;
- memcpy(beg, buf, numOfOldItemsToKeep * sizeof(T));
+ if (buf) memcpy(beg, buf, numOfOldItemsToKeep * sizeof(T));
free(buf);
buf = static_cast<T *>(p);
}
=====================================
test/last-test.out
=====================================
@@ -26,7 +26,7 @@
#
# name start alnSize strand seqSize alignment
#
-# Query sequences=0
+# Query sequences=0 normal letters=0
TEST lastal -fMAF -u1 -j5 -p ../data/HOXD70.mat -z3400 -e2500 /tmp/last-test galGal3-M-32.fa
#
# a=400 b=30 A=400 B=30 e=2500 d=1311 x=3400 y=962 z=3400 D=1e+06 E=2.80488e+07
@@ -139,7 +139,7 @@ s chr32 0 1028 + 1028 CATCTAAACCAACACCTAATCCTAAACCTAAGGCCTTCCGGAATCCTAAACCTAAGCC
s chr32 0 1028 + 1028 CATCTAAACCAACACCTAATCCTAAACCTAAGGCCTTCCGGAATCCTAAACCTAAGCCAACAGctaaccctaacccatcccctaacccaatccatagccctaagcttaagcctaaccctaagccaaaccctagccctaaccatagccccaactccagcactaaccgtaatggtaaacttaatgataatcctaaccctaacacaaaccctTCTTTCCGGAGCTGGGGAAACCGACTCCAGAAATGCCATCTGAGGGAACAGACGTCCTGGCAGATAGAACAAACCAGGTGTGAGCACTGTCTTTCCAAAGTTACACCGAAGCCGTTGGAGGACAGGTCGGACCTCAGGCCTTCCCGCGGCACCAACTACTGTCGGCGGATTTGCGCATAGATCCTTCACAGCTGTTTCAAAGAACCATTCTGTGATTCTATGATCTTCCAGGACCCTTCCAAGCCACACCATCCTGTGGTTCTatcatcttccaggactcttgcaacacaaaccattctatggttctgtgatCACTAAGGAACCTCCCAAGCCACGCCGTCCTGCAGTTCTGtgatcttccaggacccttccaacacggaccatcctatggttctatgatCTTCCAGGACCCTCCTGTGCGGGTGATGTCACCATGACGTGATGACCTCACAGATGCCCTGGGGTGGGGCAGGGGCAGTGGGTCAGCGCGGAACCTGCTGGCCCCATTCTGCGGGTGGTGCTGGTCCAGCGAGGAGCTGTGCGAGTGGTGCAGTAATGCGGGCCCAGTGTGTCAGCAGAAGATTAAGGGCGGTGTGGCGTGCGAAGCTGGTGGAGGAGGAGCTGCTGGTGAGCTCTGGGTGCACAGACACAGAAGGGCCGGCGGGGGGAGCTGCCGGCTGGAGGCAGCAGAGGGCCGGGCACCTCCGGTGGGATGCAGAGCTGCCGGCAGCACCTCGGTGCCAACGCTGCTCCTCTCCCTTCACACAGGCTCATGCGGCCGTGGAGAAGTGCAAGGCCGTGGCCAGGGAATCCTTGATG
p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# Query sequences=2
+# Query sequences=2 normal letters=17803
>chrM
AATTTTATTTTTTAACCTAACTCCCCTACTAAGTGTACCCCCCCTTTCCCCAGGGGGGGTATACTATGCATAATCGTGCATACATTTATATACCACATATATTATGGTACCGGTAATATATACTATATATGTACTAAACCCATTATATGTATACGGGCATTAACCTATATTCCACATTTCTCCCAATGTCCATTCTATGCATGATCTAGGACATACTCATTTACCCTCCCCATAGACAGTTCCAAACCACTATCAAGCCACCTAACTATGAATGGTTACAGGACATAAATCTCACTCTCATGTTCTCCCCCCAACAAGTCACCTAACTATGAATGGTTACAGGACATACATTTAACTACCATGTTCTAACCCATTTGGTTATGCTCGCCGTATCAGATGGATTTATTGATCGTCCACCTCACGAGAGATCAGCAACCCCTGCCTGTAATGTACTTCATGACCAGTCTCAGGCCCATTCTTTCCCCCTACACCCCTCGCCCTACTTGCCTTCCACCGTACCTCTGGTTCCTCGGTCAGGCACATCCCATGCATAACTCCTGAACTTTCTCACTTTTCACGAAGTCATCTGTGGATTATCTTCCCCTCTTTAGTCCGTGATCGCGGCATCTTCTCTCTTCTATTGCTGTTGGTTCCTTCTCTTTTTGGGGCTTCTTCACAGGTTACCCTTCACAGTGCGGGTGCGAGTGCTATTCAAGTGAAGCCTGGACTACACCTGCGTTGCGTCCTATCCTAGTCCTCTCGTGTCCCTCGATGAGACGGTTTGCGTGTATGGGGAATCATCTTGACACTGATGCACTTTGGATCGCATTTGGTTATGGTTCTTCCACCCCCCCGGTAAATGGTGCTATTTAGTGAATGCTTGTCGGACATATTTTTATCAATTTTCACTTCCTCTATTTTCTTCACAAAACTAGGAAATTCACCACAAttttttctttgttattttttaattttttttttattttttAAAAACATTTTTTAAAAAACTAAATTACATACAAACTACCGCATAAAATCCCTCAAACTATACAAACGTTTATCGTATAATATATATACATTATTGTTTATTCTATCATTATTAGAGAAACTCCACTACCAAAACCATCATTAAAACAAAAATTTACATGCCACTTAACTCCCCTCACAAACAATCGTTATTTATATTGTTAATTAGCAAACACAAAACCCGCCTTCTACCACTATAAAGCCCCCATAGCTTAACCCACAAAGCATGGCACTGAAGATGCCAAGATGGTACCTACTATACCTGTGGGCAAAAGACTTAGTCCTAACCTTTCTATTGGTTTTTGCTAGACATATACATGCAAGTATCCGCATCCCAGTGAAAATGCCCCCAAACCTTTCTTCCCAAGCAAAAGGAGCAGGTATCAGGCACACTCAGCAGTAGCCCAAGACGCCTTGCTTAAGCCACACCCCCACGGGTACTCAGCAGTAATTAACCTTAAGCAATAAGTGTAAACTTGACTTAGCCATAGCAACCCAGGGTTGGTAAATCTTGTGCCAGCCACCGCGGTCATACAAGAAACCCAAATCAATAGCTACCCGGCGTAAAGAGTGGCCACATGTTATCTGCACCAGCTAAGATTAAAATGCAACCAAGCTGTCATAAGCCTAAGATCCACCTAAACCCAACCCAAATCCATCTTAGCCTCAACGATTAATTTTAACCCACGAAAGCTAGGACCCAAACTGGGATTAGATACCCCACTATGCCTAGCCCTAAATCTAGATACCTCCCATCACACATGTATCCGCCTGAGAACTACGAGCACAAACGCTTAAAACTCTAAGGACTTGGCGGTGCCCCAAACCCACCTAGAGGAGCCTGTTCTATAATCGATAATCCACGATTCACCCAACCACCCCTTGCCAGCACAGCCTACATACCGCCGTCGCCAGCCCACCTCTAATGAAAGAACAACAGTGAGCTCAATAGCCCCTCGCTAATAAGACAGGTCAAGGTATAGCCTATGGGGTGGGAGAAATGGGCTACATTTTCTAACATAGAACAAACGAAAAAGGATGTGAAACCCGCCCTTAGAAGGAGGATTTAGCAGTAAAGTGAGATCATACCCCCTAAGCTCACTTTAAGACGGCTCTGAGGCACGTACATACCGCCCGTCACCCTCTTCACAAGCCATCAACATCAATAAATATATACTTCCCCTCCCGGCTAAAGACGAGGCAAGTCGTAACAAGGTAAGTGTACCGGAAGGTGCACTTAGACTACCAAGGCGTAGCTATAACTTCAAAGCATTCAGCTTACACCTGAAAGATACCCTCAACAGACAAGGTCGCCTTGACTTGCCCCCCCTCTAGCCCGACAAACTCGTACCCTTAACATAAAAAACTTACCTCCCCCTCTTAACCAAAACATTATAAATTGTCCCAGTATAGGCGATAGAAAAGACTACCCCGGCGCAATAGAGGCTAACTGTACCGCAAGGGAAAGATGAAATAGCAATGAAAACCATAAGCAAAAAACAGCAAAGACCAACCCTTGTACCTTTTGCATCATGATTTAGCAAGAACAACCAAGCAAAGTGAGCTAAAGTTTGCCTTCCCGAAACCCAAGCGAGCTACTTGCGAGCAGCTAAAATTTGAGCGAACCCGTCTCTGTTGCAAAAGAGCGGGATGACTTGCCAGTAGAGGTGAAAAGCCTACCGAGCTGGGTGATAGCTGGTTACCTGTCAAACGAATCTAAGTTCCCCCTTAACCCACCCCCTAAAGACACCCACCTTTGTCAACCTTGAGAACGTTGGGGTTAAGAGCAATTCGATGGGGGTACAGCTCCATCGAAAAAGAACACAACCTCCTCCAGCGGATAATAATCACCCCTCCCCGCACTGTGGGCCTTCAAGCAGCCACCAACAAAAGAGTGCGTCAAAGCTCCCTCATTAAAAAATCTAAAACCCTATTTGACTCCCTCAACCAAAGCAGGTTAACCTATGACAATAGAAGAATCAATGCTAAAATGAGTAATCTGGAACCTATCCTCCTACGGCGTAAACTTACATTAATACATTATTAACAGAACTCAACTTATACCCCCACACTAACAAGCAATACGTATTCCTCAATCTGTTAAGCCAACCCAGGAGCGCCCACAGGATGATTAAAACCTACAGAAGGAACTCGGCAAACCAAAGACCCGACTGTTTCCCAAAAACATAGCCTTCAGCTAACAACAAGTATTGAAGGTGATGCCTGCCCAGTGACCCCCAAAGTTCAACGGCCGCGGTATCCTAACCGTGCGAAGGTAGCGCAATCAATTGTCCCGTAAATTGAGACTTGTATGAATGGCTAAACGAGGTCTTAACTGTCTCCTGTAGGTAATCTATGAAATTAGTATTCCCGTGCAAAAACGAGAATGTGAACATAAGACGAGAAGACCCTGTGGAACTTTAAAATCACGACCACCTTACAACCTTACACAGCCCCACTGGGTCCACCCACACATAAACCCCTGGTCGACATTTTTCGGTTGGGGCGACCTTGGAGAAAAAAAAATCCTCCAAACCCACAGACCACAACTCTTCACTAAGACCAACTCCTCAAAGTACCAACAGTAACCAGACCCAATATAATTGAGCAATGGACCAAGCTACCCCAGGGATAACAGCGCAATCTCCTCCAAGAGCCCATATCGACAAGGAGGTTTACGACCTCGATGTTGGATCAGGACAACCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTTCAACGATTAACAGTCCTACGTGATCTGAGTTCAGACCGGAGCAATCCAGGTCGGTTTCTATCTATGGACACTCCTCCTAGTACGAAAGGACCGGAGAAGTGGGGTCAATACCACTGAGCACACCCCAACCTTCTAAGCAATGAATACAACTCAACTGCCAAGAACCCCTCCCCCACACCCGAACTCCTAGAAAAGGATCCAGCTAGCGTGGCAGAGCTCGGCAAATGCAAAAGGCTTAAGCCCTTTATCCAGAGGTTCAAATCCTCTCCCTAGCTACCCCGGACATGACCCTGCCCACCCTAACAAACCTTCTAATCATAACCTTATCCTATATTCTCCCCATCCTAATCGCCGTGGCCTTCTTAACACTTGTAGAACGAAAAATCCTAAGCTACATGCAGGCCCGAAAGGGCCCAAACATTGTGGGCCCTTTTGGTCTACTCCAACCCGTTGCAGACGGGGTAAAACTATTCATTAAAGAGCCAATCCGACCATCTACCTCCTCCCCCTTCCTCTTCATTATTACTCCAATCCTAGCACTACTCCTAGCCCTGACTATTTGAGTCCCCCTCCCACTACCATTCCCCCTTGCAGACCTCAACCTAGGACTACTATTTCTCCTAGCCATATCAAGCCTAACTGTCTACTCTCTACTCTGATCCGGATGAGCATCAAACTCCAAGTATGCCCTAATCGGAGCCCTTCGAGCCGTCGCACAAACAATCTCATACGAAGTCACCCTAGCCATCATCCTGTTATCCACAATCATACTGAGCGGCAATTACACCTTAAGCACCCTGGCCATCACCCAAGAGCCCATCTACCTCATTTTTTCCGCATGACCCCTCGCAATAATATGATACATCTCTACCCTTGCTGAAACCAACCGCGCCCCATTTGACCTAACAGAAGGAGAGTCAGAGCTAGTCTCAGGATTTAATGTAGAATATGCCGCCGGACCATTCGCCATATTCTTCTTAGCCGAATACGCCAACATTATACTAATAAACACACTAACCACCGTCCTATTCCTGAACCCAAGCTTCCTAAATCTCCCACCAGAATTATTTCCCATTGCACTCGCTACAAAAACCCTCCTCCTTTCATCCTCATTTCTATGAATCCGGGCCTCATATCCACGGTTCCGCTATGACCAACTAATACATCTTCTATGAAAAAACTTCCTCCCCCTAACCCTAGCCTTATGCCTCTGACATACCAGCATACCAATCAGCTACGCCGGCCTCCCCCCAATCTAAGGAAGCGTGCCTGAACAAAAAGGATCACTATGATAAAGTGAACATAGAGGTATAACAACCCTCTCACTTCCTTAATCCTAGAAAAGTAGGAATCGAACCTACACAGAAGAGATCAAAACTCTTCATACTCCCTCTATATTATTTTCTAGTAAGGTCAGCTAACTAAGCTATCGGGCCCATACCCCGAAAATGATGGTTTAACCCCTTCCCCTACTAATGAACCCCCATGCAAAACTAATCTGCACAGTAAGCCTCATCATGGGAACCAGCATCACAATCTCCAGCAACCATTGAATCTTAGCCTGAACAGGCTTAGAGATCAACACCTTAGCCATCATCCCCCTCATCTCCAAGTCACACCACCCCCGAGCGATTGAAGCCACTATCAAATATTTCCTCACCCAATCAACTGCATCAGCCCTAATCCTCTTCTCGAGCATAACCAACGCCTGATCCACCGGACAATGAGACATTACACAACTAAACCACCCGACATCATGCCTAATATTAACAATAGCAATCGCAATCAAATTAGGACTAGTCCCATTCCACTTCTGATTCCCAGAAGTACTCCAAGGCTCCTCCCTAATCACTGCCCTACTACTCTCCACCCTAATAAAACTCCCCCCAATCACACTCCTCCTCCTAACATCACAGTCTCTTAATACCACCTTACTCACCCTCCTAGCAATCTCCTCCACCCTAATCGGAGGCTGAATGGGCCTAAACCAAACACAAACACGAAAAATCCTAGCCTTCTCATCCATCTCCCATTTAGGATGAATAATTATAATTATCTCCTATAACCCACAACTCACTATTCTCACCTTCATCCTCTACACAATTATGACCTCAACTGTATTCCTATCCCTAGCCCAAATCAAAGTCCTAAAACTGTCAACACTACTCATCTCATGAACTAAAACCCCAATACTAAATGCAACTGTAATACTAACCCTCCTCTCCCTAGCTGGCCTCCCACCATTAACCGGCTTCATGCCAAAATGACTCATTATCCAAGAACTAACCAAACAAGAAATAACCCCAATAGCCACAATCATCACAATACTATCACTCCTAAGCCTATTCTTCTACCTCCGACTTGCATACCACTCAACAATCACACTCCCCCCCAACTCATCAAACCACATAAAACTCTGACGAACTAACAAAACCCTAAACACCCCCACCGCCATTCTAACTGCGCTATCAACCACCCTATTGCCCCTTTCCCCCCTAATTATTACCATACTATAGAAACTTAGGATTAACTGTCACCAAACCAAAGGCCTTCAAAGCCTTAAATAAGAGTTAAACTCTCTTAGTTTCTGCCCAACTAAGACCAACAGGACATTAACCTGTATCTCCTGAATGCAAATCAGACGCTTTAATTAAGCTAAGGCCTCTACCTAGACAGATGGGCTTCGATCCCATACAATTTTAGTTAACAGCTAAATGCCAACACCAATTGGCTTCTGCCTACAGACCCCGGCACACTTTAGTGTACATCAACGAGTTTGCAACTCATTATGAACTTCACTACAGAGTCGATAAGAAGAGGAATTGAACCTCTGTAAAAAGGACTACAGCCTAACGCTTCAACACTCAGCCATCTTACCTGTGACCTTCATCAACCGATGATTATTCTCAACCAACCACAAAGACATTGGCACTCTTTACCTAATTTTCGGCACATGGGCGGGCATAGCCGGCACAGCACTTAGCCTTCTAATTCGCGCAGAACTAGGACAGCCCGGAACTCTCTTAGGAGACGATCAAATTTACAATGTAATCGTCACAGCCCATGCTTTCGTCATAATCTTCTTTATAGTTATACCCATCATGATCGGTGGCTTCGGAAACTGACTAGTCCCACTTATAATCGGTGCCCCAGACATAGCATTCCCCCGCATAAATAACATAAGCTTCTGACTCCTCCCTCCCTCCTTCCTTCTCCTACTAGCCTCATCTACCGTAGAAGCTGGGGCCGGCACAGGATGGACAGTTTACCCCCCTTTAGCCGGCAACCTAGCCCACGCTGGCGCATCAGTAGACCTAGCCATCTTTCATTACTTAGCAGGTGTTTCCTCCATTCTAGGAGCCATCAACTTTATCACTACCATCATCAACATAAAACCCCCCGCACTGTCACAATACCAAACACCCCTATTCGTATGATCCGTCCTCATTACTGCCATCCTACTACTCCTCTCCTTACCCGTCCTAGCAGCTGGGATTACCATACTACTTACCGACCGCAACCTTAACACCACATTCTTCGACCCAGCTGGAGGAGGAGACCCAATCCTATACCAACACCTATTCTGATTCTTCGGTCACCCCGAAGTTTACATCCTCATCCTCCCAGGTTTCGGAATAATTTCCCACGTAGTAGCATACTATGCAGGAAAAAAAGAACCATTCGGATACATAGGAATAGTCTGAGCCATACTGTCAATCGGATTCCTTGGCTTCATTGTATGAGCCCACCATATATTCACAGTCCGAATGGACGTAGACACCCGAGCCTACTTTACATCAGCCACAATAATCATCGCCATCCCAACTGGTATTAAAGTCTTCAGCTGACTAGCAACCCTGCACGGAGGAACAATTAAATGAGACCCCCCTATGCTATGAGCCCTAGGATTCATCTTCCTCTTCACTATCGGAGGCCTAACGGGAATCGTCCTTGCTAACTCATCACTAGATATTGCCCTTCATGACACCTACTATGTAGTCGCCCACTTCCACTATGTCCTCTCAATGGGGGCAGTTTTTGCCATTCTAGCAGGATTTACCCACTGATTTCCCCTCTTCACAGGCTTTACCCTACACCCATCATGAACCAAGGCACATTTCGGAGTAATATTTACCGGAGTTAACCTAACCTTTTTCCCCCAACATTTCCTGGGCCTAGCTGGAATACCCCGACGATACTCAGATTACCCAGACGCCTACACACTATGAAACACACTATCCTCAATCGGCTCCTTAATTTCAATAACAGCCGTAATCATACTCATATTCATCGTCTGAGAAGCCTTCTCAGCAAAACGAAAAGTACTCCAACCCGAATTAACTGCCACTAATATCGAATGAATTCATGGCTGCCCACCCCCATACCACACCTTCGAAGAACCAGCCTTTGTACAAGTGCAAGAAAGGAAGGAATCGAACCCTCACATGTTGGTTTCAAGCCAACCGCATCAAACCACTTAATGCTTCTTTCTTATGAGACGTTAGTAAACCAATTACATAGACCTGTCAAGACTAAATCACAGGTGCAAACCCTGTACATCTCATATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTATCATCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATCGGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGCGGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTACTGTCATCTTAACCATTAAGAAGCTATGCACCAGCACTAGCCTTTTAAGCTAGAGAGAGGGGACACCCTCCCCCTTAATGACATGCCCCAATTAAACCCAAACCCATGATTCTCCATCATACTCCTAACTTGATTCACCTTCTCTCTGCTTATCCAACCCAAACTTCTTTCATTCACTCTAACAAACAACCCTGCAAACAAAATTACAACAACTAAACCCACCCCCTGAACCTGACCATGAACCTAAGCTTCTTCGACCAATTCTCAAGCCCCTGCCTACTAGGAATCCCTCTAATCCTCCCATCACTCCTTCTTCCAGCCCTCCTACTTCCATCACCAGGAAACCGATGGATCAACAACCGCCTCTCCACCATCCAACTCTGATTCACCCACCTAATCACAAAACAACTAATAACCCCCCTAAACAAGGCAGGTCACAAATGAGCCCTCCTACTCACCTCACTTATCCTAATACTCCTCTCCATTAACCTCCTAGGCCTCCTCCCCTACACCTTCACCCCAACTACCCAACTATCAATAAACATGGCCTTAGCCCTGCCACTATGACTAGCCACCTTACTAACAGGCCTGCGAAACCAACCCTCCGCCTCCTTAGGACACCTACTCCCTGAAGGCACCCCCACCCCACTGATTCCAGCCCTAATCATAATCGAAACAACCAGCCTACTTATTCGGCCATTAGCCCTAGGAGTACGCCTAACAGCAAACCTCACAGCTGGTCACCTACTTATCCAACTTATCTCTACAGCCACAATCGCCCTACTACCAATAATGCCATCAATCTCCGCCCTAACGGCACTCATCCTATTCCTACTAACCATCCTAGAAGTGGCAGTAGCAATAATCCAAGCCTACGTCTTCGTCCTCCTCCTAAGCCTCTACTTACAAGAAAATATTTAATGGCACACCAAGCACACTCCTACCACATAGTTGACCCAAGCCCATGACCAATCTTCGGCGCAGCCGCAGCACTACTAACCACCTCTGGCCTAATCATATGGTTCCACTACAGCTCGACCACCCTACTGACAATAGGCCTCCTCTCTATACTTCTAGTCATGCTGCAATGATGACGAGACGTAGTCCGAGAAAGCACCTTCCAGGGCCACCACACCCCAACTGTCCAAAAGGGCCTACGATACGGAATAATCCTTTTCATTACATCAGAGGCCTTCTTCTTCCTAGGATTCTTCTGAGCCTTCTTCCACTCAAGCCTAGCCCCAACACCAGAACTGGGGGGCCAATGGCCCCCAACAGGAGTCAAACCCCTAAACCCCCTTGAAGTACCCCTACTAAATACAGCAATCCTCCTAGCCTCAGGAGTCACCGTTACATGGGCTCACCACAGCATCACAGAAGGAAACCGAAAACAAGCCATCCACGCACTAACTCTCACAATCCTCCTAGGATTCTATTTCACAGCCCTACAAGCAATAGAGTACCATGAAGCCTCCTTCTCAATCGCTGACAGCGTCTACGGCTCCACCTTCTTCGTCGCTACAGGGTTCCACGGACTACATGTAATCATTGGATCATCCTTTTTAACAGTTTGCCTCCTACGACTAATCAAATTCCACTTCACACCAAACCACCACTTCGGATTTGAAGCAGCAGCCTGATACTGACACTTCGTAGACATCATCTGACTCTTCCTCTACATATCCATATACTGATGAGGATCTTGCTCTTCTAGTATACTCATTACAACTGACTTCCAATCTTTAAAATCTGGTATCAACCCAGAGAAGAGCAATGAACACACTTACATTTATACTCTCACTATCCTTTCTACTAAGCGCTGCACTAACTACTATAAACTTTTGACTAGCCCAAATAGCCCCAGACACAGAAAAACTGTCACCGTACGAATGCGGATTTGACCCACTAGGATCAGCCCGACTCCCATTCTCAATCCGATTCTTCCTAGTAGCCATCCTATTCCTTTTATTCGACCTAGAAATCGCCCTGCTTCTTCCCCTTCCATGAGCCATCCAACTTGCACACCCTATAATAACCCTTACTTGAGCCACCACTATCATCGCCCTCCTCACATTTGGTCTCATCTACGAATGAACTCAGGGCGGCTTAGAATGAGCAGAATAACAGAAAGTTAGTCTAACTAAGACAGCTGGTTTCGACCCAGCAAATTATAGACCCACCTATAACTTTCTTATGTCTCCCCTACACTTCAGCTTCTATTCTGCATTCACATTCAGCAGCCTAGGACTAGCATTCCACCGAACACACCTCATCTCTGCCCTACTATGCCTAGAGAGCATAATACTATCCATATTCATCCCCCTCTCAATCTGACCAGTAGAAAACCAAACCCCATCATTCGCCCTTGTACCTATCCTAATACTAGCCTTCTCAGCATGCGAAGCTGGCACAGGCCTAGCCATACTAGTAGCTTCTGCACGAACACATGGCTCTGACCACCTACACAACCTAAACCTTCTACAATGCTAAAGATCATCCTACCAACAATCATACTCTTGCCCACAGCCCTCTTATCCCCAGCAAAATCCATATGAACTAACACCACAATATACAGCCTTCTAATCGCCTCGATCAGCCTACACTGACTAACCCCATCATACTACCCCACAAAAACCCTAACCCTCTGAACAGGCATAGACCAAATCTCAACTCCCCTCTTAGTACTCTCCTGCTGGTTTCTCCCCCTCATAATTATAGCTAGCCAAGGCCACCTACAACATGAACCCCACAAACGAAAACGAATATTCATCTCCACCTTAATCATCATCCAACCATTCATCATCCTAGCCTTCTCAGCAACTGAACTCATACTATTCTACATCTCATTCGAAGCAACCCTAATCCCAACCCTCATCTTAATCACACGCTGAGGAAACCAACCAGAACGACTTAGCGCAGGCATTTACCTTCTATTCTATACCCTAATTAGCTCTCTTCCCCTACTAGTCTCCATCCTCTACCTTCACACAAATACTGGAACCCTCCACCTACCCATTATCAAACTCACCCACCCCAACCTACCTGCCTCCTGAACAAGCTTATTATCTAGCCTAGCTCTCCTAATAGCCTTTATAGTCAAAGCACCCCTATACGGACTACACCTATGACTGCCTAAAGCCCATGTAGAAGCACCAATCGCAGGCTCCATACTACTCGCTGCTCTACTACTAAAACTAGGCGGATATGGCATCATACGAGTCACCCTCCTAATGGAGCCCGTATCCAACTTCTTACACTACCCCTTCCTCACCCTAGCCCTATGAGGTGCCCTAATAACTAGCTCTATCTGCTTACGCCAAACAGACCTAAAATCCCTCATTGCCTACTCATCCGTAAGCCATATGGGCCTAGTCATCGCTGCAAGTATAATCCAAACCCAATGATCATTCTCAGGTGCAATAATCCTCATAATCTCCCATGGACTAACCTCTTCCCTTTTATTCTGCCTAGCAAACACAAACTACGAACGGACACACAGCCGCATTCTTATCCTGACACGAGGCCTCCAACCCCTCCTACCATTGATATCAGTATGATGATTACTAGCCAACTTAACCAACATGGCCCTGCCCCCAACCACCAACCTGATAGCAGAACTAACAATTATAGTTGCCCTCTTCAACTGATCCTCCCCCACAATTATCTTAACCGGCACTGCAACACTCCTAACCGCCTCTTACACCCTCTACATACTACTCTCAACCCAACGAGGCACTCTTCCATCCCACATCACAACAACCCCCAACTCAAACACTCGAGAACATCTTCTCATAACCCTCCACATCATCCCCATACTAACACTCATCCTCAAACCAGAACTAATCTCAGGAACCCCTCTATGCAAACATAGTTTAACCCAAACATTAGATTGTGATTCTAAAAATAGGAGTTTAACCCTCCTTGTTCGCCGAGGGGAGGCCCAAGCCAGCAAGAACTGCTAATTCCTGCATCTGAGCTTTAAACCTCAGTCCCCTTAACTTTTAAAGGATAAGAGCAATCCGTTGGTCTTAGGAACCACCTATCTTGGTGCAAATCCAAGTAAAAGTAATGGAGACTCCACTGCTCCTTAACACCCTCACAACATTAACACTACTCACCCTCCTTACCCCTATTATCCTTCCCCCCCTCCTAAATCTAAAAAACTCCCCCATATCCATCACCAAAACCATTAAAACCGCCTTCCTAATCAGCCTAATCCCAACAACAATCTTCATCCACTCAGGGGCAGAAAGCATTGCCACCCACTGAGAATGACAATTTATCCCCAACTTCAAGATCCCCATCTCCCTAAAAATAGACATATACTCCATAATATTCTTCCCCATTGCACTATTTGTAACCTGATCCATCTTAGAGTTCGCAACATGATACATAGCATCCGAACCATTTATTACAAAATTCTTTACCTACCTACTCACCTTCCTCATCGCCATATTAACACTAACCATCGCAAATAACATATTCCTCCTATTTGTAGGATGAGAAGGAGTAGGAATCATGTCATTCCTTCTCATTGGATGATGACAAGGACGAGCTGAAGCCAACACAGCTGCACTACAGGCAATAATCTACAACCGAATCGGAGACATTGGCCTCATCCTAAGCATAGCATGACTAGCCTCTTCCCTAAACACCTGAGAAATTCAACAAATCACCCACCCAAACCAAACACCCACCCTCCCCCTCCTTGGCCTAATCCTAGCCGCCACAGGAAAATCCGCTCAATTTGGCCTTCACCCATGACTTCCAGCAGCAATAGAAGGCCCAACCCCTGTCTCCGCCCTACTCCATTCCAGCACAATAGTAGTTGCTGGAATTTTTTTACTCATCCGCACCCACCCCTTCCTGTCATCCAATAAAACAGCCCTGACAACGTGCCTATGCTTAGGTGCTCTATCAACACTCTTTGCCGCAACATGCGCTCTCACTCAAAACGACATCAAAAAAATCATTGCCTTCTCCACTTCAAGCCAACTAGGCCTCATAATAGTCACAATTGGCCTAGACCTCCCCCAACTAGCCTTCCTCCACATCTCAACCCATGCCTTCTTTAAAGCTATATTATTCCTATGCTCCGGCCTAATTATCCACAGCCTCAATGGAGAACAAGACATCCGCAAAATAGGATGTCTACAAAAAACCCTCCCAATAACCACCTCCTGCCTAACCATTGGCAACCTCGCTCTAATAGGAACTCCATTCCTAGCAGGCTTCTACTCAAAAGACCTGATCATCGAAAACCTAAACACCTCATACATCAATACCTGAGCCCTCTCACTTACACTACTTGCCACATCTTTCACTGCAACCTACAGCCTCCGCATAACCTTACTAGTCCAAACAGGACACACACGAACCCCCAGCAATCACCCCATTAACGAAAACACCCCCCCAGCCATTCTCCCAATCATACGACTAGCCCTTGGCAGCATTATAGCAGGCCTATTAATCTCATCCCTAATCCTCCCCCCTAAAACCCCTCCAATAACTATACCCACCATCACAAAAACTGCTGCCATCATTGTTACAACCCTAGGAATTATCCTAGCCCTAGAACTCTCAAGCCTATCATACTCCCTCACTCCCCCAAAACACAATCCCCTCATAAACTTCTCCTCCTCCCTAGGCTACTTTAACCCCCTAACTCACCGAATTAGCCCCTCAATCCTCCTACATACCGGACAAAAAATTGCATCCCACTTAATCGACATAGCATGGTACAAAAAAATAGGCCCCGAAGGCCTTGCCAACCTTCATCTCACCATAACCAAAATCTCAACCACACTCCACACAGGCCTAATTAAATCTTACCTGGGTTCCTTCGCCCTCACAATCCTTACAACGATCCTACTTATCCAAAAATAAACTAATGGCACCCAACATTCGAAAATCCCACCCCCTACTAAAAATAATTAACAACTCCCTAATCGACCTCCCAGCCCCATCCAACATCTCTGCTTGATGAAATTTCGGCTCCCTATTAGCAGTCTGCCTCATGACCCAAATCCTCACCGGCCTACTACTAGCCATGCACTACACAGCAGACACATCCCTAGCCTTCTCCTCCGTAGCCCACACTTGCCGGAACGTACAATACGGCTGACTCATCCGGAATCTCCACGCAAACGGCGCCTCATTCTTCTTCATCTGTATCTTCCTTCACATCGGACGAGGCCTATACTACGGCTCCTACCTCTACAAGGAAACCTGAAACACAGGAGTAATCCTCCTCCTCACACTCATAGCCACCGCCTTTGTGGGCTATGTTCTCCCATGGGGCCAAATATCATTCTGAGGGGCCACCGTTATCACAAACCTATTCTCAGCAATTCCCTACATTGGACACACCCTAGTAGAGTGAGCCTGAGGGGGATTTTCAGTCGACAACCCAACCCTTACCCGATTCTTCGCTTTACACTTCCTCCTCCCCTTTGCAATCGCAGGTATTACTATCATCCACCTCACCTTCCTACACGAATCAGGCTCAAACAACCCCCTAGGCATCTCATCCGACTCTGACAAAATTCCATTTCACCCATACTACTCCTTCAAAGACATTCTGGGCTTAACTCTCATACTCACCCCATTCCTAACACTAGCCCTATTCTCCCCCAACCTCCTAGGAGACCCAGAAAACTTCACCCCAGCAAACCCACTAGTAACCCCCCCACATATCAAACCAGAATGATATTTTCTATTCGCCTATGCCATCCTACGCTCCATCCCCAACAAACTTGGAGGTGTACTAGCCCTAGCAGCCTCAGTCCTCATCCTCTTCCTAATCCCCTTCCTCCACAAATCTAAACAACGAACAATAACCTTCCGACCACTCTCCCAAACCCTATTCTGACTTCTAGTAGCCAACCTTCTTATCCTAACCTGAATCGGAAGCCAACCAGTAGAACACCCCTTCATCATCATTGGCCAAATAGCATCCCTCTCTTACTTCACCATCCTACTTATCCTCTTCCCCACAATCGGAACACTAGAAAACAAAATACTCAACTACTAAAATACTCTAATAGTTTATGAAAAACATTGGTCTTGTAAACCAAAAACTGAAGACTCCACCCTTCTTAGAGTATCAGAAAAGGAGGGCTCAAACCTCCATCTCCAGCTCCCAAAGCTGGTATTTTCAAATAAACTACTCTCTGAAACCCTTAAACCGCCCGAATTGCCCCCCGAGACAACCCACGCACAAGCTCTAGTACAACAAACAAAGCTAACAACAAACCTCACCCAGCCACCAAAAACAACCCAACCCCACATGAATAAAACACCGCAACTCCACTAAAATCCAACCGAGCAAAAGACACACCCCCGCCATCAACAGTAACCACCCCCACCTTTCAAAAATCAACGAGCCCTCCCAGAACCACCCCCATTCAAACCACCAAGACAAAACCTAGCCCATACCCCACCACCCGCCAATCCCCCCAAGCCTCAGGATAAGGATCCGCAGCTAATGACACAGAATAAACAAAAACCACCAACATCCCCCCTAAATACACCAAAAATAACGCCAAGGAAACAAAAGAAACACCCAAACTCACTAACCACCCACATCCTATCACAGACGCTACCACCAACCCCACCACCCCATAATACGGCGAAGGATTAGACGCCACAGCTAAAACCCCCAGCATAAAACAAATCCCAAGAAAAATCACAAAATAAGTCATATTATTCCCGCTTGGTTAGACCCCAAGGACTACGGCTTGAAAAGCCATTGTTGTTCTCAACTACGGGAAC
@@ -189,7 +189,7 @@ TEST lastal -fTAB -i1 -w0 -e40 /tmp/last-test galGal3-M-32.fa
44 chr32 51 158 + 1028 chr32 3 158 + 1028 158 EG2=0.00038 E=1.3e-14
42 chr32 3 138 + 1028 chr32 69 138 + 1028 138 EG2=0.0034 E=1.1e-13
42 chr32 69 138 + 1028 chr32 3 138 + 1028 138 EG2=0.0034 E=1.1e-13
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -j0 -i1 -s0 /tmp/last-test galGal3-M-32.fa
#
@@ -232,7 +232,7 @@ chr32
11 2
12 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -Q1 -e90 -a9 /tmp/last-test SRR001981-1k.fastq
#
@@ -329,7 +329,7 @@ s chrM 959 27 + 16775 gttattttttaattttttttttatttt
s SRR001981.815 1 25 - 36 GTTTTTGTTT--TTTTTTTTTTATTTT
q SRR001981.815 23+)03/+<I--G,I'9I/D3+IEII7
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -F12 -pBL62 -e40 -G ../examples/vertebrateMito.gc -j1 /tmp/last-test galGal3-M-32.fa
#
@@ -413,7 +413,7 @@ s Q2LCP8 0 34 + 491 MVCLFENLMNMIKYSIYILPLIILIVLSISIKKD
s chrM 196 102 - 16775 LVSLGVSFVSLALFLVYLGGMLVVFVYSVSLAAD
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -F12 -pBL62 -e40 -G2 -j1 /tmp/last-test galGal3-M-32.fa
#
@@ -497,7 +497,7 @@ s Q2LCP8 0 34 + 491 MVCLFENLMNMIKYSIYILPLIILIVLSISIKKD
s chrM 196 102 - 16775 LVSLGVSFVSLALFLVYLGGMLVVFVYSVSLAAD
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
#
@@ -533,7 +533,7 @@ TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
19 chrM 4168 33 + 16775 chrM 12574 33 - 16775 33 EG2=3e+08 E=0.09
18 chrM 31 34 + 16775 chrM 16710 34 - 16775 34 EG2=9.1e+08 E=0.27
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -s0 -f0 -p asymmetric.mat -e2000 /tmp/last-test galGal3-M-32.fa
#
@@ -570,7 +570,7 @@ TEST lastal -s0 -f0 -p asymmetric.mat -e2000 /tmp/last-test galGal3-M-32.fa
2089 chr32 690 217 + 1028 chrM 6958 219 - 16775 43,0:4,138,2:0,34 EG2=6.4e+07 E=0.019
2060 chr32 721 195 + 1028 chrM 7144 192 - 16775 91,3:0,101 EG2=8.5e+07 E=0.025
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -Q3 -e110 /tmp/last-test illumina100.txt
#
@@ -612,7 +612,7 @@ s chr32 97 40 + 1028 ccctaagcttaagcctaaccctaagccaaaccctagccct
s HWW-E2:1:1:10:1477#0/1 10 40 + 50 CCCTAACCCTAANCCTAACCCTAACCCTAACCCTAACCCT
q HWW-E2:1:1:10:1477#0/1 aaaYaaa`aXaaB\bZ`Y_aa]_Q^b]G]O^aaS\RMX]\
-# Query sequences=100
+# Query sequences=100 normal letters=4900
TEST lastal -Q4 -e90 /tmp/last-test mouse_tss_prb.txt
#
@@ -669,7 +669,7 @@ s chrM 2016 26 + 16775 GGTGGG-AGAAATGGGCTACATTTTCT
s 36 0 27 + 36 GGTGGGAAGAAATGGGCTACATTTTCT
q 36 hhhhhhhhhhhhhhhhhhhhhhhhhhh
-# Query sequences=100
+# Query sequences=100 normal letters=3600
TEST lastal -Q1 -j6 -e90 -a9 /tmp/last-test SRR001981-1k.fastq
#
@@ -777,7 +777,7 @@ q SRR001981.815 3+)03/+<I--G,I'9I/D3+IEII7
p $$$$$$%&&&&~~~~~~~~~~~~~~~
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -r3 -q3 -a21 -c2 -e60 -f0 /tmp/last-test galGal3-M-32.fa
#
@@ -819,7 +819,7 @@ TEST lastal -r3 -q3 -a21 -c2 -e60 -f0 /tmp/last-test galGal3-M-32.fa
78 chrM 6570 46 + 16775 chrM 12733 46 - 16775 46 EG2=1e+05 E=6.1e-05
# batch 1
3084 chr32 0 1028 + 1028 chr32 0 1028 + 1028 1028 EG2=0 E=0
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -F12 -pBL62 -c2 -e40 -f0 /tmp/last-test galGal3-M-32.fa
#
@@ -881,7 +881,7 @@ TEST lastal -F12 -pBL62 -c2 -e40 -f0 /tmp/last-test galGal3-M-32.fa
40 Q2LCP8 133 57 + 491 chrM 14165 168 - 16775 15,2:0,1,0:1,15,2:9,16,0:-1,6 EG2=2.2e+11 E=3.4
40 Q2LCP8 406 20 + 491 chrM 2209 60 - 16775 20 EG2=2.2e+11 E=3.4
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -j1 -f0 -e37 -m100 /tmp/last-test Q2LCP8.fa
#
@@ -938,7 +938,7 @@ TEST lastal -j1 -f0 -e37 -m100 /tmp/last-test Q2LCP8.fa
47 Q2LCP8 110 69 + 491 Q2LCP8 278 69 + 491 69 EG2=3.4e+10 E=0.0071
55 Q2LCP8 255 96 + 491 Q2LCP8 324 96 + 491 96 EG2=2.6e+09 E=0.00052
37 Q2LCP8 7 46 + 491 Q2LCP8 391 46 + 491 46 EG2=8.7e+11 E=0.19
-# Query sequences=1
+# Query sequences=1 normal letters=491
TEST lastal -Q1 -r1 -q2 -a1 -b1 -e44 -m100 -s0 /tmp/last-test sd-ccs-100.fq
#
@@ -987,7 +987,7 @@ q S1_55 ?-;F8)M='&1-J+1B(&-27B&,@<L.917D'=/>Q*55,7?)4%H7DFD1>F8.8.
s S1_100 0 239 - 239 TCATTATGCAAAGTGGT-TGGATCTGTTTTATGCCGGATTCA-TAATAATCTGCCGCCGCTGCGTTTTGTGCGTAATCTCGGGTTAATGGCGG-CAGAGCGTGCTGGCGTGTT-AAACGTCAGGCGCTGAAAT-TGCGTTAGGGTTGTAGCCTTACAACATTGCCGGATGCGTGCCAACCGTAGGTCGGATAAGACGCGGCAG-GTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCA
q S1_100 <i~'a;><q<f*`kduZ-LNlIBn at -2KH*~aLG44oC+H9]-A at 9;WJ7.P~L?1h~/NVmp~HNfFOKEJ=m4V_FT<JrD}WR(FFNs~N-I:EBI)HP`US8,+R>~;N-B*xC?h_I~O4MIaS<9C/- at wSQk6F[^$9S~f4i87PTP6E<OvDJ=XN~0_N;HFR;*FaK~AEQUJQWU\oH]~~OU_a<H;VOT-?ZrXPI\~w&@f7bP~?LNFN+\HUS:lI5]l;b at mN\~5<
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -Q1 -e90 -a9 -f0 /tmp/last-test0 SRR001981-1k.fastq
#
@@ -1035,7 +1035,7 @@ TEST lastal -Q1 -e90 -a9 -f0 /tmp/last-test0 SRR001981-1k.fastq
90 chrM 971 15 + 16775 SRR001981.805 21 15 + 36 15 EG2=6.8e+08 E=0.00044
91 chrM 959 27 + 16775 SRR001981.815 1 25 - 36 10,2:0,15 EG2=5.5e+08 E=0.00035
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
#
@@ -1071,7 +1071,7 @@ TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
19 chrM 4168 33 + 16775 chrM 12574 33 - 16775 33 EG2=3e+08 E=0.09
18 chrM 31 34 + 16775 chrM 16710 34 - 16775 34 EG2=9.1e+08 E=0.27
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
#
@@ -1107,7 +1107,7 @@ TEST lastal -s0 -f0 -e18 /tmp/last-test galGal3-M-32.fa
19 chrM 4168 33 + 16775 chrM 12574 33 - 16775 33 EG2=3e+08 E=0.09
18 chrM 31 34 + 16775 chrM 16710 34 - 16775 34 EG2=9.1e+08 E=0.27
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -T1 -Q1 -e60 -a9 -f0 /tmp/last-test SRR001981-1k.fastq
#
@@ -1146,7 +1146,7 @@ TEST lastal -T1 -Q1 -e60 -a9 -f0 /tmp/last-test SRR001981-1k.fastq
60 chrM 950 36 + 16775 SRR001981.597 0 36 - 36 19,2:0,10,1:0,4,0:3 EG2=5.6e+11 E=0.5
# batch 3
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -T1 -Q1 -e60 -a9 -j4 /tmp/last-test SRR001981-1k.fastq
#
@@ -1206,7 +1206,7 @@ p ))*++,111.,((++,,,,0/~~~~~~~~~~(&&&%).)
# batch 3
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -T1 -Q1 -e60 -j1 -fTAB /tmp/last-test SRR001981-1k.fastq
#
@@ -1246,7 +1246,7 @@ TEST lastal -T1 -Q1 -e60 -j1 -fTAB /tmp/last-test SRR001981-1k.fastq
# batch 2
# batch 3
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -s0 -e18 -j7 /tmp/last-test galGal3-M-32.fa
#
@@ -1309,7 +1309,7 @@ p (+./~~~~~~~~~~BA@@@@@@@@@?=:62-,*'
c 4.89 0.00223 0.25 0.93 2.08 8.23 2 0.247 0.963 3.26e-07 8.23 0.00218 0.711 0.945 2.08 4.91 36.5 0.00322 0.00317 0.00194 0.00191
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -T1 -Q1 -e60 -a9 -f0 /tmp/last-test SRR001981-1k.fastq
#
@@ -1358,7 +1358,7 @@ TEST lastal -T1 -Q1 -e60 -a9 -f0 /tmp/last-test SRR001981-1k.fastq
# batch 3
77 chrM 673 27 + 700 SRR001981.815 0 25 - 36 11,2:0,14 EG2=1.2e+10 E=0.00037
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -e34 -k128 -f0 /tmp/last-test galGal3-M-32.fa
#
@@ -1398,7 +1398,7 @@ TEST lastal -e34 -k128 -f0 /tmp/last-test galGal3-M-32.fa
95 chrM 1742 281 + 16571 chrM 2432 295 + 16775 26,0:1,12,0:4,25,0:4,11,0:2,57,1:0,42,0:1,24,0:3,83 EG2=2e-28 E=1.1e-37
48 chrM 14425 318 + 16571 chrM 16456 319 + 16775 247,0:2,54,1:0,16 EG2=4.8e-06 E=2.6e-15
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -pHOXD70 -e4500 -k128 -f0 /tmp/last-test galGal3-M-32.fa
#
@@ -1434,7 +1434,7 @@ TEST lastal -pHOXD70 -e4500 -k128 -f0 /tmp/last-test galGal3-M-32.fa
58424 chrM 14729 1565 + 16571 chrM 14874 1560 + 16775 23,0:1,7,0:2,1121,0:2,25,1:0,31,0:6,14,4:0,20,0:2,49,17:0,19,2:0,8,0:8,18,1:0,18,0:14,35,3:0,31,0:1,21,9:0,2,3:0,9,1:0,24,0:1,19,0:4,15,5:0,10 EG2=2e-223 E=8.2e-233
8383 chrM 14155 588 + 16571 chrM 16213 562 + 16775 121,3:0,23,2:0,23,4:0,64,5:0,10,4:0,2,9:0,118,2:0,8,0:2,14,0:1,5,1:0,99,0:2,54,1:0,16 EG2=3.9e-18 E=2.1e-27
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -e34 -C2 -f0 /tmp/last-test galGal3-M-32.fa
#
@@ -1474,7 +1474,7 @@ TEST lastal -e34 -C2 -f0 /tmp/last-test galGal3-M-32.fa
95 chrM 1742 281 + 16571 chrM 2432 295 + 16775 26,0:1,12,0:4,25,0:4,11,0:2,57,1:0,42,0:1,24,0:3,83 EG2=2e-28 E=1.1e-37
48 chrM 14425 318 + 16571 chrM 16456 319 + 16775 247,0:2,54,1:0,16 EG2=4.8e-06 E=2.6e-15
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -e34 -f0 -l30 /tmp/last-test galGal3-M-32.fa
#
@@ -1513,7 +1513,7 @@ TEST lastal -e34 -f0 -l30 /tmp/last-test galGal3-M-32.fa
251 chrM 2409 754 + 16571 chrM 3112 772 + 16775 41,2:0,38,0:1,32,0:2,37,0:3,235,0:6,58,0:1,39,0:6,15,0:1,148,0:1,53,1:0,55 EG2=1.1e-102 E=5.9e-112
95 chrM 1742 281 + 16571 chrM 2432 295 + 16775 26,0:1,12,0:4,25,0:4,11,0:2,57,1:0,42,0:1,24,0:3,83 EG2=2e-28 E=1.1e-37
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -j0 -l4 -L11 -s0 /tmp/last-test galGal3-M-32.fa
#
@@ -1546,7 +1546,7 @@ chr32
10 12
11 2
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -e5 -f0 /tmp/last-test ttttt.fa
5 tttttccccc 0 5 + 10 ttttt 0 5 + 5 5 EG2=1.4e+15 E=0.02
@@ -1605,7 +1605,7 @@ a score=95 EG2=2e-28 E=1.2e-37
s chrM 2432 295 + 16775 AGTATAGGCGATAGAAAAGACTACCCCGGCGCAATAGAGGCTAACTGTACCGCAAGGGAAAGATGAAATAGCAATGAAAACCATAAGCAAAAAACAGCAAAGACCAACCCTTGTACCTTTTGCATCATGATTTAGCAAGAAC-AACCAAGCAAAGTGAGCTAAAGTTTGCCTTCCCGAAACCCAAGCGAGCTACTTGCGAGCAGCTAAAATTTGAGCGAACCCGTCTCTGTTGCAAAAGAGCGGGATGACTTGCCAGTAGAGGTGAAAAGCCTACCGAGCTGGGTGATAGCTGGTT
s chrM 1742 281 + 16571 AGTATAGGCGATAGAAATTGAAACCT-GGCGCAATAGAT----ATAGTACCGCAAGGGAAAGATGAAA----AATTATAACCA--AGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGA-CGAGCTACCTAAGAACAGCTAAAA---GAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTT
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -e40 -u3 -fTAB /tmp/last-test hg19-M.fa
#
@@ -1644,7 +1644,7 @@ TEST lastal -e40 -u3 -fTAB /tmp/last-test hg19-M.fa
160 chrM 3629 255 + 16775 chrM 2908 255 + 16571 146,1:0,53,0:1,55 EG2=2.3e-59 E=1.3e-68
122 chrM 3112 338 + 16775 chrM 2409 334 + 16571 41,0:2,38,1:0,32,2:0,37,3:0,184 EG2=2.8e-41 E=1.6e-50
95 chrM 2432 295 + 16775 chrM 1742 281 + 16571 26,1:0,12,4:0,25,4:0,11,2:0,57,0:1,42,1:0,24,3:0,83 EG2=2e-28 E=1.2e-37
-# Query sequences=1
+# Query sequences=1 normal letters=16571
#
# a=29 b=2 A=28 B=1 e=119.332 d=63 x=119 y=47 z=119 D=1e+06 E=2.80852e+07
@@ -1679,7 +1679,7 @@ TEST lastal -e40 -u3 -fTAB /tmp/last-test hg19-M.fa
247.4 chrM 16213 562 + 16775 chrM 14155 588 + 16571 135,0:27,75,0:5,29,5:0,246,2:0,54,0:1,16 EG2=4.8e-05 E=2.9e-14
127.3 chrM 14396 89 + 16775 chrM 8953 95 + 16571 35,0:9,13,3:0,38 EG2=5.3e+06 E=0.0031
121.1 chrM 7217 72 + 16775 chrM 3316 72 + 16571 72 EG2=1.9e+07 E=0.011
-# Query sequences=1
+# Query sequences=1 normal letters=16571
#
# a=29 b=2 A=28 B=1 e=86.6721 d=63 x=86 y=47 z=86 D=1000 E=2.80852e+10
# R=01 u=2 s=2 S=1 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.72795 j=3 Q=1
@@ -1743,7 +1743,7 @@ s SRR001981.832 14 21 + 36 AGGTGAGTGATAGTTGGTTAC
q SRR001981.832 =IIII at IIIII2III,?IIH8
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -e100 /tmp/last-test Q5GS15.fa
#
# a=11 b=2 A=11 B=2 e=100 d=31 x=99 y=31 z=99 D=1e+06 E=2.01411e+09
@@ -1789,7 +1789,7 @@ a score=376 EG2=1.1e-33 E=1.8e-47
s Q2LCP8 23 416 + 491 LIVLSISIKKDVQRVHIIIQSLKLtlivimiviGIEESIYVKLNGHLIKTELIKLFEYLLLGVSYMIIKMFEEGVTEGKKTKITDEGLILIYSSIIGMLISMEAHNLITLFLSLEISSICFYILA-LNKNSRKGIEGGLKYYIIGGIATTILLLGIVSIYKSTGSLMYTDLLVIVMENTDDYRIQMGIALIVLGLILKLGIAPFHGWLIDVYEGAGMLMTFYLTITQKlvtlmvlinlyqnliiytnaimftngliILILVTLVVGTIGSLRQQKLIRFIAYSAIVNSALLILMLAGSMSEELMVNSVYYLINYIIGLTVLMSLIMGFLRLNDRGTIEDIYQLKNMWVINMFGAIVYILVLMYLAGLPPMTNFISKILILLPYMVLGRVYLTMLAFFLSVGVMIYYMNLVKIIIIDK
s sp|Q5GS15|NUON_WOLTR 16 405 + 465 LVLLLLGIVFNRRTINLLALGCTVITLIILI-LSAKDSGFFPFNSLLKLDLYIRSAQGLILIAGILvllllnls-----kydyeyefsililfTLFGMITLVSANNLISFYLSFELMSIPLYVLASFNKDSVYSCEAGVKYFTLSALSSCIMLYGMSllygytglvnfselssfleNHQMTYGIVFGLVLILIGLCFKLAIAPFHMWAPDVYQGAPTIVTAFFSTVPKAALVTFLIRFFMGEELVGVEKYFQPVLLYISALSVLISAFGALRQRNLKRLLAYSSIGHIGFILASLS-IFTRMGTDSSLIYLVIYII---TNIGLFSYFIQIDDDDC--SVANLSGIGKKRPVLAFHLSILLFSMAGIPPLAGFFAKLFIFKSLVNSGFIGMSLIFIVASVISCYYYLSIIKAMYFDK
-# Query sequences=1
+# Query sequences=1 normal letters=465
TEST lastal -F15 -pBLOSUM62 -e100 /tmp/last-test galGal3-M-32.fa
#
@@ -1837,7 +1837,7 @@ s Q2LCP8 110 321 + 491 LILIYSSIIGMLISMEAHNLITLFLSLEISSICFYILALNKNSRKGIEGGLKYY
s chrM 5258 870 + 16775 LICTVSLIMGTSITISSNH*ILA*TGLEINTLAIIPLISKSHHPRAIEATIKYFLTQSTASALILFSSITNA*STGQ*DITQL-----------NHPTSCLILTIAIAIKLGLVPFHF*FPEVLQGSSLITALLLSTLIKLPPITLLLLTSQSL----Nttllt---llaISSTLIGG*MG-LNQTQTRKILAFSSISHLG*IIIII--SYNPQLTI--LTFILYTIMTSTVFLSLAQ--IKVLKLSTL--LIS*TKTPILN----ATVILTLLSLAGLPPLTGFMPK*LIIQELTKQEITPiatiitilsllslfFYLRL
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -pAT77 -e100 -s0 /tmp/last-test at-rich.fa
#
@@ -1949,7 +1949,7 @@ a score=243 EG2=6.3e-19 E=2.3e-27
s Pf3D7_01_v3 53773 763 + 59940 ATATTTATTCATTTAATAATTTTGTGTATTGGGCTTTTTTCTTCATTTTtttttTTCGTCGATAACGTAAAATCAAATAAATTATTATCATAATTAAAACTATAATTAATATGGCAAGGATGGTGTAACCAATTGTGGTGTaccaattgTAAATTGTAGCTTCCATAACTTGCTCTTGTGCTTCTTCAATAGCTAATTTATTAGCAGCTTCAGCAGTCTTagcagcGGCTT------TAGCTGATACTTCGGCTTCTGACATCATAGTTTCTACAGTTCTTTTTATAACTTCTTCATGTGAAATATATTGTCCTCTTTGTGATACAGCTGAAATTTGTTTCCACACCGAATTGCAAATACCAATATGACGGTTAACGTCACCGAAAGAGGATAACAGGTTCCTTGAAGGATCATATACACATATCTCATAATGTTGTCCATAAACAGCTTTAGTAATGCTCGAGACATTTTTATAAGATATTGTTCTAAAAAAGGATTTCAATGTCTGACCTTTTAGAGTTGATATACCCATTTTTTGTAATTCTGCAATAACTAATGCCTTACCTATAACCTCACCCGCAGCATTAGCGGCagcCGCAATCTTAACAGCATTTGCATTTAGAGCTGCTgTAatagcggcaTCAAGTGCCGCAGGTTTCCATATATTTATAGCAACCGCACCAAATAAT-CCAATACTTCC--------TGcaacacttcctAGCCCACATC-----CACACCTAAGACAACCTTTTTCTATTTTTTCTGCTAAGTTTTTCTC
s Pf3D7_01_v3 8300 748 - 59940 ATATTTATTCTTCTAATAATTTTATATATTGGAGTTTTTTCTTCAATTTCATTTTTCTGCGATAACGTAAAATCAAATATATTATAACCATAATTAAAACTATGATTACTATTGCAACGATGG---ATGCTATTATAGGAGTATAGTAGGAAGTAGTTGCAGCTTCTACTTCGGCTATGTTTTTTGCTGTA---AATTCTGTTGTATATATAGGAGTCATGACCGCAGTTTTGGTAGTAGCAGCTTGTTCAGCTCCTGCAACagctTcTTCTACCTTTTCATATATAATAGTTTGTGCTGAA---------CTTCTATAAAAACTACCTTGAAGATTTGAATGAACCAAATTGCAAAAAGGATCACTAGTGTTAAAAGTACCGACA------AGCTGATCATTAACTAAACTAGGTGTACATGACGTGGTATAATGAGAATAAACTTTATCATAAATGAAAGACACATTCATATAATTTGTTACATCAATAATTGTTTCCAATAGTTTATCACCTACAAAGTATATACCCAATGTGCGTAATTGTTCAATAACAGCATTAGTACCTGCCAAATGTCCTGCTTTAAGACCTGctgct------------gcAcctgcTTGTTTAGCTAATTCCATAGCCGCTGCAATTTCTGTAGTTTTCCACACACTTAGCGCAGCTTCAGAAATTCCTGCTAATACTCCTGAAGAGGGTGCAACAAT--CTTTCCCAAATTTTGCGTACATTTCAAACAATTTTTTTCCACTTTATCTGCTAATGATTTTTC
-# Query sequences=1
+# Query sequences=1 normal letters=59940
TEST lastal -Q1 -a15 -b3 -e80 /tmp/last-test nano.fq
#
@@ -1987,7 +1987,7 @@ s channel_100_read_89_2 4684 34 + 6457 CAGCAACCAATGGATCTTACGC-GACCAGGATGAG
q channel_100_read_89_2 +)*+*'()')(''*()((()*+-()&'('''*''(
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=13060
@S1_1
TAAATCCATAAGTATTACTCGGCAGAAGAGGTTTGATGTCGGCGAGCTGTTTCTCCAGCCCGGCAATACGCTGTTGTAGTTGCCAACGGGGAGTCATGGTTTTGCATTCCCCATCCCCGCTCCGGGCGGTAAAGCGTGGCCAAATCCACAAAAATGGCCAGATAACATGCAGCGTAAAAAGATCACCCAACCAGCAACATGAATGGCGTCGGCATGGGATGATTACGTTTTTTAGCATCAGGTAGGGAATATCATTAAAATAATAATCCCATAGAATATCACCAGAAATACAAAAATAAGCACTCCCAGTGCAAAATAATCCAGAAACATATTTCCCTCAGAGATATAAAAAAGAACAATTAACGCATATTATGAAATCCCATGATGCAGTGCAATTTCCTTATTTATATAACGGCATATTGTTTTTTATATACTTTCTGAAGTGTGCTGCGTGGCTTTTCAACGGTCGAGGTTTATCATATTGAAATAATGGAACTATTGACCAAGCTAATGAATAACTCCAGTAAAACATCCACAGTACAGTAAAGCGTATTAAACCTTCAATTATCTACCGTTTATTGCTGATTGGCCTCGGAACGCCAATGGTGATTTACGGCTGGTTTGCCCGCTCACCATCGAAACGCGAGAGTAAACTCCTGGCAAAACACGCCCCAGAAACGCATTCTGTTGGCGTAGTCTGGGTTATTGCGCACGTAGGTTTAAAACGTAAATTGTAACAACGT
@@ -2436,7 +2436,7 @@ q S1_77 4r=ShVl8SDFTR:\-ZAK=?KnOPb`SUWBI--)R~7O6D-%'@`V760BIQ5?U
s chrM 1295 63 + 16775 CAAAAGACTT-AGTCCTAACC--TTT-CTATTGGTTTTTGCTAGACATATACATGCAAGTATCCGCA
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -Q4 -a1 -D100 /tmp/last-test mouse_tss_prb.txt
lastal: quality data not used for non-fastq query versus fastq reference
@@ -2505,7 +2505,7 @@ q S1_58 ~~nQl~VTkqlxmP~k~~{4X>~
s 94 17 19 + 36 GCGCGGAGGAGG---ACGG-GGG
q 94 hhhhhhhhhXhh---hhhh-FB]
-# Query sequences=100
+# Query sequences=100 normal letters=3600
TEST lastal -Q1 -pBL62 -F12 -D1000 /tmp/last-test sd-ccs-100.fq
lastal: quality data not used for DNA-versus-protein alignment
@@ -2674,7 +2674,7 @@ a score=41 EG2=1.6e+11 E=0.077
s Q2LCP8 344 15 + 491 SLIMGFLRLNDRGTI
s S1_99 437 45 + 621 TLTMGFMPVNPRATI
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -Q1 -pBL62codon.mat -F12 -t3.08611 -e36 -d29 /tmp/last-test sd-ccs-100.fq
lastal: quality data not used for DNA-versus-protein alignment
@@ -2872,7 +2872,7 @@ s Q2LCP8 344 15 + 492 SerLeuIleMetGlyPheLeuArgLeuAsnAspArgGlyThrIle
s S1_99 437 45 + 621 ACCCTGACGATGGGTTTCATGCCTGTAAATCCCCGGGCCACCATT
q S1_99 BE>R;B61+*C9,QB%C[BJ?EL2HT;JEa48D4H-:*J=CaMHO
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -Q1 -pbadcodon.mat -a17 -F0 -j4 -X1 -D1000 /tmp/last-test sd-ccs-100.fq
lastal: quality data not used for DNA-versus-protein alignment
@@ -3044,7 +3044,7 @@ s S1_98 4 39 + 401 ATTGCGTCATTCGCGTCGCTTGTGATGTCACCAATCCGC
q S1_98 yq{~I8V.~S~XFRM~Sp~~B~?a[bDI~~~aRo~JsTK
p '''))),,,222333~~~~~~===:::777111///(((
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -Q1 -pbadcodon.mat -a17 -b1 -F9,9,9,9 -X1 -D1e3 -j4 /tmp/last-test sd-ccs-100.fq
lastal: quality data not used for DNA-versus-protein alignment
@@ -3240,7 +3240,7 @@ s S1_93 119 36 - 650 CTCAAAGCCATCCTGGTGATGATTATGGTGGTCATT
q S1_93 ?_sI~R_lA`PhDjXLL>'am3:HU<5[<JQ6aVXJ
p ~~~~~~888999:::555555555333...---***
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -Q1 -pBL62 -b1 -F3,3,3,3 -X1 -j4 -e56 /tmp/last-test sd-ccs-100.fq
lastal: quality data not used for DNA-versus-protein alignment
@@ -3463,7 +3463,7 @@ s Q2LCP8 344 15 + 492 SLIMGFLRLNDRGTI
s S1_99 437 45 + 621 TLTMGFMPVNPRATI
p &+/~~~?:<=8731,
-# Query sequences=100
+# Query sequences=100 normal letters=45801
>Q2LCP8
MVCLFENLMNMIKYSIYILPLIILIVLSISIKKDVQRVHIIIQSLKLtlivimiviGIEESIYVKLNGHLIKTELIKLFEYLLLGVSYMIIKMFEEGVTEGKKTKITDEGLILIYSSIIGMLISMEAHNLITLFLSLEISSICFYILALNKNSRKGIEGGLKYYIIGGIATTILLLGIVSIYKSTGSLMYTDLLVIVMENTDDYRIQMGIALIVLGLILKLGIAPFHGWLIDVYEGAGMLMTFYLTITQKlvtlmvlinlyqnliiytnaimftngliILILVTLVVGTIGSLRQQKLIRFIAYSAIVNSALLILMLAGSMSEELMVNSVYYLINYIIGLTVLMSLIMGFLRLNDRGTIEDIYQLKNMWVINMFGAIVYILVLMYLAGLPPMTNFISKILILLPYMVLGRVYLTMLAFFLSVGVMIYYMNLVKIIIIDKVQTHEQGVAELEITSKPTKGGRRIVLGVMWLIFSQLYLDEILNVIKVIVALI*
@@ -3576,7 +3576,7 @@ s Q2LCP8 183 10 + 492 SerThrGlySerLeuMetTyrThrAspLeu
s S1_92 157 30 + 283 CCCATTGGCCTGTTGATGTATGCCAATCTG
q S1_92 8AFN8I??GG](>Q=CNG/G>@(;^X49RH
-# Query sequences=100
+# Query sequences=100 normal letters=45801
TEST lastal -fBlastTab -pBL62 -b1 -F15 -D1e3 /tmp/last-test galGal3-M-32.fa
#
@@ -3663,7 +3663,7 @@ chrM Q2LCP8 50.00 12 6 0 8526 8561 18 29 14 20
chrM Q2LCP8 50.00 10 5 0 1314 1343 225 234 14 20
# batch 1
chr32 Q2LCP8 23.21 56 42 1 43 210 8 62 0.59 20.5
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -fBlastTab+ -pBL62 -b1 -F15 -D1e3 /tmp/last-test galGal3-M-32.fa
#
@@ -3750,7 +3750,7 @@ chrM Q2LCP8 50.00 12 6 0 8526 8561 18 29 14 20 16775 491 36
chrM Q2LCP8 50.00 10 5 0 1314 1343 225 234 14 20 16775 491 36
# batch 1
chr32 Q2LCP8 23.21 56 42 1 43 210 8 62 0.59 20.5 1028 491 37
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -j4 -pBL62 -b1 -F0 -D1e3 /tmp/last-test galGal3-M-32.fa
#
@@ -4034,7 +4034,7 @@ s Q2LCP8 7 55 + 491 LMNMIKYSIYILPLIILIVLSISIKKDVQRVHIIIQSLKLtliv-imiviGIEESI
s chr32 42 168 + 1028 ILNLSQQLTLTHpltqsialslsltlsqtlaltiaptpaltvmvnlmiiltltqtl
p #$$$$$$#$$%&~~-+*+***))'$#"""!""""""###$$###"#$$$$$$$##"
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -S1 -pBISF -Q1 -e120 -f0 -j4 /tmp/last-test bs100.fastq
#
@@ -4161,7 +4161,7 @@ TEST lastal -S1 -pBISF -Q1 -e120 -f0 -j4 /tmp/last-test bs100.fastq
259 chrM 569 65 + 16571 97 0 65 + 87 65 EG2=7.7e-09 E=6.7e-21 fullScore=272
223 chrM 6938 71 + 16571 98 16 71 - 87 71 EG2=2.9e-05 E=3.3e-17 fullScore=235
290 chrM 8939 87 + 16571 99 0 87 - 87 87 EG2=6.4e-12 E=4.1e-24 fullScore=302
-# Query sequences=100
+# Query sequences=100 normal letters=8700
TEST lastal -D1000 -fTAB -K2 /tmp/last-test galGal3-M-32.fa
#
@@ -4343,7 +4343,7 @@ TEST lastal -D1000 -fTAB -K2 /tmp/last-test galGal3-M-32.fa
15 chrM 13147 33 + 16571 chr32 78 33 + 1028 33 EG2=2.4e+10 E=0.8
15 chrM 1676 23 + 16571 chr32 71 23 + 1028 23 EG2=2.4e+10 E=0.8
15 chrM 6590 19 + 16571 chr32 2 19 + 1028 19 EG2=2.4e+10 E=0.8
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -D1000 -fTAB -K0 /tmp/last-test galGal3-M-32.fa
#
@@ -4429,7 +4429,7 @@ TEST lastal -D1000 -fTAB -K0 /tmp/last-test galGal3-M-32.fa
15 chrM 13147 33 + 16571 chr32 78 33 + 1028 33 EG2=2.4e+10 E=0.8
15 chrM 1676 23 + 16571 chr32 71 23 + 1028 23 EG2=2.4e+10 E=0.8
15 chrM 6590 19 + 16571 chr32 2 19 + 1028 19 EG2=2.4e+10 E=0.8
-# Query sequences=2
+# Query sequences=2 normal letters=17803
TEST lastal -W19 -fTAB /tmp/last-test hg19-M.fa
#
@@ -4479,7 +4479,7 @@ TEST lastal -W19 -fTAB /tmp/last-test hg19-M.fa
25 chrM 3973 69 + 16775 chrM 3237 70 + 16571 38,0:1,31 EG2=4.2e+05 E=0.00025
22 chrM 12073 105 + 16775 chrM 12976 102 + 16571 69,3:0,33 EG2=1.1e+07 E=0.0066
24 chrM 6570 28 + 16775 chrM 13264 28 - 16571 28 EG2=1.3e+06 E=0.00074
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -W1 -M -fTAB /tmp/last-test hg19-M.fa
#
@@ -4528,7 +4528,7 @@ TEST lastal -W1 -M -fTAB /tmp/last-test hg19-M.fa
42 chrM 5620 47 + 16775 chrM 5336 50 + 16571 3,1:0,4,0:1,3,0:1,2,0:1,2,0:1,8,1:0,8,0:1,15 EG2=2.2e+07 E=0.013
42 chrM 9034 64 + 16775 chrM 8312 68 + 16571 24,0:1,7,1:0,6,0:1,6,0:1,1,0:1,1,0:1,18 EG2=2.2e+07 E=0.013
46 chrM 6575 23 + 16775 chrM 13269 23 - 16571 23 EG2=2.5e+06 E=0.0015
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -fTAB -j4 -A2 -B2 /tmp/last-test hg19-M.fa
#
@@ -4581,7 +4581,7 @@ TEST lastal -fTAB -j4 -A2 -B2 /tmp/last-test hg19-M.fa
22 chrM 12073 105 + 16775 chrM 12976 102 + 16571 69,3:0,33 EG2=1.2e+07 E=0.0069 fullScore=24.7
22 chrM 14801 78 + 16775 chrM 14065 78 + 16571 78 EG2=1.2e+07 E=0.0069 fullScore=25.8
24 chrM 6570 28 + 16775 chrM 13264 28 - 16571 28 EG2=1.3e+06 E=0.00077 fullScore=25.6
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -fTAB -j4 -Q1 -e90 -a7 -A12 -B4 /tmp/last-test SRR001981-1k.fastq
#
@@ -4629,7 +4629,7 @@ TEST lastal -fTAB -j4 -Q1 -e90 -a7 -A12 -B4 /tmp/last-test SRR001981-1k.fastq
90 chrM 971 15 + 16775 SRR001981.805 21 15 + 36 15 EG2=9.9e+08 E=0.00062 fullScore=91.3
93 chrM 959 27 + 16775 SRR001981.815 1 25 - 36 10,2:0,15 EG2=5.1e+08 E=0.00031 fullScore=101
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -fTAB -j4 -Q0 -e90 -a7 -A12 -B4 -b9 -r6 -q18 /tmp/last-test SRR001981-1k.fastq
#
@@ -4671,7 +4671,7 @@ TEST lastal -fTAB -j4 -Q0 -e90 -a7 -A12 -B4 -b9 -r6 -q18 /tmp/last-test SRR00198
90 chrM 971 15 + 16775 SRR001981.805 21 15 + 36 15 EG2=9.9e+08 E=0.00062 fullScore=91.2
90 chrM 971 15 + 16775 SRR001981.815 11 15 - 36 15 EG2=9.9e+08 E=0.00062 fullScore=99
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -j4 -Qkeep -e90 -a7 -A12 -B4 -b9 -r6 -q18 /tmp/last-test SRR001981-1k.fastq
#
@@ -4749,7 +4749,7 @@ q SRR001981.815 G,I'9I/D3+IEII7
p ~~~~~~~~~~~~~~~
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
TEST lastal -N2 /tmp/last-test hg19-M.fa
#
@@ -4793,7 +4793,7 @@ a score=24 EG2=1.3e+06 E=0.00074
s chrM 6570 28 + 16775 GTCGATAAGAAGAGGAATTGAACCTCTG
s chrM 13264 28 - 16571 gttgttaagaagaggaattgaacctctg
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST tr Tt Uu < hg19-M.fa | lastal -N2 /tmp/last-test
#
@@ -4837,7 +4837,7 @@ a score=24 EG2=1.3e+06 E=0.00074
s chrM 6570 28 + 16775 GTCGATAAGAAGAGGAATTGAACCTCTG
s chrM 13264 28 - 16571 gttgttaagaagaggaattgaacctctg
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -W19 -z50% -fTAB /tmp/last-test hg19-M.fa
#
@@ -4905,7 +4905,7 @@ TEST lastal -W19 -z50% -fTAB /tmp/last-test hg19-M.fa
25 chrM 3973 69 + 16775 chrM 3237 70 + 16571 38,0:1,31 EG2=4.2e+05 E=0.00025
22 chrM 2478 22 + 16775 chrM 1783 22 + 16571 22 EG2=1.1e+07 E=0.0066
24 chrM 6570 28 + 16775 chrM 13264 28 - 16571 28 EG2=1.3e+06 E=0.00074
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -W19 -x1g -fTAB /tmp/last-test hg19-M.fa
#
@@ -4952,7 +4952,7 @@ TEST lastal -W19 -x1g -fTAB /tmp/last-test hg19-M.fa
26 chrM 856 48 + 16775 chrM 198 48 + 16571 48 EG2=1.4e+05 E=8.3e-05
26 chrM 5538 94 + 16775 chrM 12989 94 + 16571 94 EG2=1.4e+05 E=8.3e-05
24 chrM 6570 28 + 16775 chrM 13264 28 - 16571 28 EG2=1.3e+06 E=0.00074
-# Query sequences=1
+# Query sequences=1 normal letters=16571
TEST lastal -L9 -m0 -j1 -q0 -d5 -n6 -fTAB /tmp/last-test tttttccccc.fa
#
@@ -4980,7 +4980,7 @@ TEST lastal -L9 -m0 -j1 -q0 -d5 -n6 -fTAB /tmp/last-test tttttccccc.fa
6 chrM 3866 9 + 16775 tttttccccc 0 9 - 10 9
8 chrM 4223 9 + 16775 tttttccccc 0 9 - 10 9
7 chrM 8832 9 + 16775 tttttccccc 0 9 - 10 9
-# Query sequences=1
+# Query sequences=1 normal letters=10
TEST lastal -Q1 -T1 -j1 -s0 /tmp/last-test SRR001981-1k.fastq
#
@@ -5094,7 +5094,7 @@ s SRR001981.873 11 25 - 36 GAAGTATGACATTCCATATTCTGAC
q SRR001981.873 IIIIIIIIIIIIHIIIIIIIIIIII
# batch 4
-# Query sequences=1000
+# Query sequences=1000 normal letters=35941
#
# a=10 b=1 A=10 B=1 e=36 d=20 x=35 y=18 z=35 D=1e+06 E=7.76903e+08
@@ -5130,7 +5130,7 @@ a score=558 EG2=1.7e-115 E=5e-132
s LTR22B1#LTR/ERVK 0 521 + 526 TGTGGGGGTTCAGTCAGGNTGGTGGGAAAAATTNTAAGACGNAGTTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGAAGGTTTTGCANAAGCCTCAGGATAGGGTTATGGCTGAAGGCAGCCTAATC--CTTACCTTGAGTTA-ATAGCTTAGGGTAGNTAACANAGGAATGTAGAGGAGTTTATCTAAAT-AGCTTGTTTACTCATGTGGTCCTAAGACCAACCTTTGATCATCCGCGGGTGCATGATTGCTCTCTACTCGGGNGCGGGGGTGGGCAATCGGCAACCAGGTTAATTACCCTCTAGTGGTGTTTACTCGAGACCTTTGTCATTTNNCGNNNAATCTGTGCTGAATAAATGCNAGCNNNGCCGGCTAGTCGGGGCCGCGGCTG---CNACTCTTTACAGCACCCTCCTTGGNGTCTGTGAGCGGCCCGGACCCTCAGCCGGACTGACA-GGCANAATATCTGTGTC--AGTGTACGTTATTCATCCGTCGTTGGGTCAGGGTCTGCGGGACGGACCC
s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGGAGGTTTTGCAAAAGCTTCAGNAAAGGGTT-TGGCTGAAGGCAGCCGAATCCTCTTANCTTGAGTTANANAGCTNAGGGTAGATANCAAAGGAATGTAAAGGAGTTTATCTAAATGNGCTTGTTTACTCATGTGGTCCTAAGACCGACCTTTGATCAT--TTGTGCGCAGGACTGCTCTCTNCTCGGGG----------------GGCGGCCATGTTAATTACCCACAAGTNGTGTTGACTCGAGGCCTTTGTCATT-------AAATCTGTACTGAATAAATGCCCGCAGCGCCAGCTTGTCAGGGCCGCGGCTGCTACAACTCTTTNCGNCGNNCGNCTNGGNNTCTGTGAGCGGCCCGGTCCCTTAGCCGCNCTGNCANNNCTGAATATCTGTGTCTGAGTGCACGTTNTTCATCCGTCGCGCGGCCAGGGTCTGCGGGTCAGACCC
-# Query sequences=1
+# Query sequences=1 normal letters=485
#
# a=10 b=1 A=10 B=1 e=36 d=20 x=35 y=18 z=35 D=1e+06 E=7.76903e+08
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=1.82048 j=3 Q=0
@@ -5164,7 +5164,7 @@ a score=572 EG2=8.1e-119 E=7e-136
s LTR22B1#LTR/ERVK 0 521 + 526 TGTGGGGGTTCAGTCAGGNTGGTGGGAAAAATTNTAAGACGNAGTTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGAAGGTTTTGCANAAGCCTCAGGATAGGGTTATGGCTGAAGGCAGCCTAATC--CTTACCTTGAGTTA-ATAGCTTAGGGTAGNTAACANAGGAATGTAGAGGAGTTTATCTAAAT-AGCTTGTTTACTCATGTGGTCCTAAGACCAACCTTTGATCATCCGCGGGTGCATGATTGCTCTCTACTCGGGNGCGGGGGTGGGCAATCGGCAACCAGGTTAATTACCCTCTAGTGGTGTTTACTCGAGACCTTTGTCATTTNNCGNNNAATCTGTGCTGAATAAATGCNAGCNNNGCCGGCTAGTCGGGGCCGCGGCTG---CNACTCTTTACAGCACCCTCCTTGGNGTCTGTGAGCGGCCCGGACCCTCAGCCGGACTGACA-GGCANAATATCTGTGTC--AGTGTACGTTATTCATCCGTCGTTGGGTCAGGGTCTGCGGGACGGACCC
s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGGAGGTTTTGCAAAAGCTTCAGNAAAGGGTT-TGGCTGAAGGCAGCCGAATCCTCTTANCTTGAGTTANANAGCTNAGGGTAGATANCAAAGGAATGTAAAGGAGTTTATCTAAATGNGCTTGTTTACTCATGTGGTCCTAAGACCGACCTTTGATCAT--TTGTGCGCAGGACTGCTCTCTNCTCGGG----------------GGGCGGCCATGTTAATTACCCACAAGTNGTGTTGACTCGAGGCCTTTGTCATT-------AAATCTGTACTGAATAAATGCCCGCAGCGCCAGCTTGTCAGGGCCGCGGCTGCTACAACTCTTTNCGNCGNNCGNCTNGGNNTCTGTGAGCGGCCCGGTCCCTTAGCCGCNCTGNCANNNCTGAATATCTGTGTCTGAGTGCACGTTNTTCATCCGTCGCGCGGCCAGGGTCTGCGGGTCAGACCC
-# Query sequences=1
+# Query sequences=1 normal letters=485
#
# a=10 b=1 A=10 B=1 e=36 d=20 x=35 y=18 z=35 D=1e+06 E=7.76903e+08
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=1.82048 j=3 Q=0
@@ -5199,7 +5199,7 @@ a score=602 EG2=6.4e-126 E=2.5e-144
s LTR22B1#LTR/ERVK 0 521 + 526 TGTGGGGGTTCAGTCAGGNTGGTGGGAAAAATTNTAAGACGNAGTTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGAAGGTTTTGCANAAGCCTCAGGATAGGGTTATGGCTGAAGGCAGCCTAATC--CTTACCTTGAGTTA-ATAGCTTAGGGTAGNTAACANAGGAATGTAGAGGAGTTTATCTAAAT-AGCTTGTTTACTCATGTGGTCCTAAGACCAACCTTTGATCATCCGCGGGTGCATGATTGCTCTCTACTCGGGNGCGGGGGTGGGCAATCGGCAACCAGGTTAATTACCCTCTAGTGGTGTTTACTCGAGACCTTTGTCATTTNNCGNNNAATCTGTGCTGAATAAATGCNAGCNNNGCCGGCTAGTCGGGGCCGCGGCTG---CNACTCTTTACAGCACCCTCCTTGGNGTCTGTGAGCGGCCCGGACCCTCAGCCGGACTGACA-GGCANAATATCTGTGTC--AGTGTACGTTATTCATCCGTCGTTGGGTCAGGGTCTGCGGGACGGACCC
s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGGAGGTTTTGCAAAAGCTTCAGNAAAGGGTT-TGGCTGAAGGCAGCCGAATCCTCTTANCTTGAGTTANANAGCTNAGGGTAGATANCAAAGGAATGTAAAGGAGTTTATCTAAATGNGCTTGTTTACTCATGTGGTCCTAAGACCGACCTTTGATCAT--TTGTGCGCAGGACTGCTCTCTNCTCGGGG----------------GGCGGCCATGTTAATTACCCACAAGTNGTGTTGACTCGAGGCCTTTGTCATT-------AAATCTGTACTGAATAAATGCCCGCAGCGCCAGCTTGTCAGGGCCGCGGCTGCTACAACTCTTTNCGNCGNNCGNCTNGGNNTCTGTGAGCGGCCCGGTCCCTTAGCCGCNCTGNCANNNCTGAATATCTGTGTCTGAGTGCACGTTNTTCATCCGTCGCGCGGCCAGGGTCTGCGGGTCAGACCC
-# Query sequences=1
+# Query sequences=1 normal letters=485
#
# a=128 b=1 A=128 B=1 e=210 d=117 x=209 y=109 z=209 D=1e+06 E=9.80233e+08
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=10.9229 j=3 Q=0
@@ -5233,7 +5233,7 @@ a score=2688 EG2=3.9e-90 E=3.6e-104
s LTR22B1#LTR/ERVK 0 521 + 526 TGTGGGGGTTCAGTCAGGNTGGTGGGAAAAATTNTAAGACGNAGTTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGAAGGTTTTGCANAAGCCTCAGGATAGGGTTATGGCTGAAGGCAGCCTAATC--CTTACCTTGAGTTA-ATAGCTTAGGGTAGNTAACANAGGAATGTAGAGGAGTTTATCTAAAT-AGCTTGTTTACTCATGTGGTCCTAAGACCAACCTTTGATCATCCGCGGGTGCATGATTGCTCTCTACTCGGGNGCGGGGGTGGGCAATCGGCAACCAGGTTAATTACCCTCTAGTGGTGTTTACTCGAGACCTTTGTCATTTNNCGNNNAATCTGTGCTGAATAAATGCNAGCNNNGCCGGCTAGTCGGGGCCGCGGCTG---CNACTCTTTACAGCACCCTCCTTGGNGTCTGTGAGCGGCCCGGACCCTCAGCCGGACTGACA---GGCANAATATCTGTGTCAGTGTACGTTATTCATCCGTCGTTGGGTCAGGGTCTGCGGGACGGACCC
s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATAGGAAATAGACACAAACCTTCTTGGAAGGCCGGGAGGTTTTGCAAAAGCTTCAGNAAAGGGTT-TGGCTGAAGGCAGCCGAATCCTCTTANCTTGAGTTANANAGCTNAGGGTAGATANCAAAGGAATGTAAAGGAGTTTATCTAAATGNGCTTGTTTACTCATGTGGTCCTAAGACCGACCTTTGATCAT--TTGTGCGCAGGACTGCTCTCTNCTCGGG----------------GGGCGGCCATGTTAATTACCCACAAGTNGTGTTGACTCGAGGCCTTTGTCATT-------AAATCTGTACTGAATAAATGCCCGCAGCGCCAGCTTGTCAGGGCCGCGGCTGCTACAACTCTTTNCGNCGNNCGNCTNGGNNTCTGTGAGCGGCCCGGTCCCTTAGCCGCNCTGNCANNNCTGAATATCTGTGTCTGAGTGCACGTTNTTCATCCGTCGCGCGGCCAGGGTCTGCGGGTCAGACCC
-# Query sequences=1
+# Query sequences=1 normal letters=485
#
# a=21 b=4 A=21 B=4 e=114 d=70 x=113 y=49 z=113 D=1e+06 E=2.92797e+07
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.88281 j=3 Q=0
@@ -5283,7 +5283,7 @@ s LTR22C#LTR/ERVK 0 505 + 509 TGTAGGGGNTCGGTCAGGGTGGTGGGAGAAATTGTAAAAATAAATTATA
130 chrM 2807 38 + 16571 chrM 3520 38 + 16775 38 EG2=1.2e+06 E=0.00064
140 chrM 3279 28 + 16571 chrM 10177 28 - 16775 28 EG2=1.5e+05 E=8.5e-05
# batch 1
-# Query sequences=2
+# Query sequences=2 normal letters=17803
#
# a=15 b=3 A=15 B=3 e=79 d=40 x=78 y=46 z=78 D=1e+06 E=1.42772e+10
# R=01 u=0 s=2 S=0 M=0 T=0 m=10 l=1 n=10 k=1 w=1000 t=4.5512 j=7 Q=0
@@ -5319,4 +5319,19 @@ s 57:130722274 0 54 + 54 AAAACCACAATGAGA---------------GTCAGAGTGGTGATTATTAA-AA
p $&'~~~~~~~~~~~~(.0233.,,,,,+--&)*+,,,-.-+++++---)'%(+253--/111/0/,,+(%
c 20.6 0.00414 1.97 1.05 1.13 4.98 0.158 2.83 0.966 0.0011 9.56 0.997 0.0153 0.0037 1.07 6.54 51.8 16.4 0.361 3 0.27
-# Query sequences=1
+# Query sequences=1 normal letters=54
+a score=192 mismap=0.117
+s KI635862 2418195 86 + 12728579 CACAGGCCGCTGCAGCCCAGAACTCCTGGCCTCAAGCGATCCACCAGCCTCAGCCTC-CGAGCAGCCGG-ATAACAGGCGCGCGCCAC
+s chr1 248803921 88 - 248956422 CATAGCTCACTGCAGCCTTGACCTCCTAGGCTAAAGCAATCCTCCCACCTTAGCCTCTCCAGTAGCTGGAACTACAGGCATGCATCAC
+p #$$%&&'(()******************************************************************************
+
+a score=330 mismap=0.75
+s KI636063 409336 105 + 789923 AAAATATGGAACGCTTCACGAATTTGCGTGTCATCCTTGCGCAGGGGCCATGCTAATCTTCTCTGTATCGTTCCAATTTTAGTATATGTGCTGCCGAAGCGAGCA
+s chr1 157784 102 + 248956422 aaaataTGGAATGCTTCACAAATTTGCATGTCATTCTTTCACAGAGGCCGTGCCAA---TCTCTCTATTGTTCCAACTTAAGTATGTGTGCTACTGAGGCAAGCA
+p !"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""!
+
+a score=203 mismap=0.0127
+s KI635862 2418239 48 + 12728579 CAGCCTCAGCCTC-CGAGCAGCC-GGATAACAGGCGCGCGCCACCGCGCC
+s chr1 248798136 50 - 248956422 CTGCCTCAGCCTCACAAGTAGCTGGGACTACAGGTGCTTGTCACCACACC
+p 33333333333333333333333333333333333322211110.*)'&$
+
=====================================
test/last-test.sh
=====================================
@@ -245,6 +245,8 @@ trap 'rm -f $db*' EXIT
# tricky Forward-Backward bug that happened once
lastdb $db alli.fa
lastal -j7 -r5 -q5 -a15 -b3 $db huma.fa
+
+ maf-cut chr1:152413-158286 split1.maf
} 2>&1 |
grep -v version | diff -u last-test.out -
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/7d8889eaba1417f5f9b837b1bbbe1746b62157fa
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/7d8889eaba1417f5f9b837b1bbbe1746b62157fa
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