[med-svn] [Git][med-team/last-align][master] 4 commits: New upstream version 1282
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Wed May 4 11:25:32 BST 2022
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
f4a6eafe by Nilesh Patra at 2022-05-04T14:40:05+05:30
New upstream version 1282
- - - - -
38cb2130 by Nilesh Patra at 2022-05-04T14:40:12+05:30
Update upstream source from tag 'upstream/1282'
Update to upstream version '1282'
with Debian dir d4c311804b8c5154b1935fe27cc2f91e9abd76dd
- - - - -
88d8ded5 by Nilesh Patra at 2022-05-04T15:08:15+05:30
Refresh patches
- - - - -
04dde6a2 by Nilesh Patra at 2022-05-04T15:10:05+05:30
Upload to unstable
- - - - -
19 changed files:
- debian/changelog
- debian/patches/simde
- doc/FAQ.rst
- doc/bisulfite.rst
- doc/last-papers.rst
- doc/last-split.rst
- doc/lastal.rst
- examples/last-bisulfite.sh
- src/lastal.cc
- src/makefile
- src/mcf_simd.hh
- src/split/last-split.cc
- src/tantan.cc
- test/SRR359290-1k.maf
- test/bs100.maf
- test/last-split-test.out
- test/maf-convert-test.out
- test/maf-swap-test.out
- test/maf-swap-test.sh
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,10 @@
+last-align (1282-1) unstable; urgency=medium
+
+ * New upstream version 1282
+ * Refresh patches
+
+ -- Nilesh Patra <nilesh at debian.org> Wed, 04 May 2022 15:09:54 +0530
+
last-align (1268-1) unstable; urgency=medium
* New upstream version 1268
=====================================
debian/patches/simde
=====================================
@@ -26,15 +26,17 @@ equivalents automatically
-
typedef __m256i SimdInt;
typedef __m256i SimdUint1;
-
-@@ -146,279 +141,6 @@ static inline SimdInt simdChoose1(SimdIn
+ typedef __m256d SimdDbl;
+@@ -181,358 +176,6 @@
+ static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
return _mm256_shuffle_epi8(items, choices);
}
-
+-
-#elif defined __SSE4_1__
-
-typedef __m128i SimdInt;
-typedef __m128i SimdUint1;
+-typedef __m128d SimdDbl;
-
-const int simdBytes = 16;
-
@@ -46,6 +48,10 @@ equivalents automatically
- return _mm_setzero_si128();
-}
-
+-static inline SimdDbl simdZeroDbl() {
+- return _mm_setzero_pd();
+-}
+-
-static inline SimdInt simdOnes1() {
- return _mm_set1_epi32(-1);
-}
@@ -58,6 +64,10 @@ equivalents automatically
- return _mm_loadu_si128((const SimdInt *)p);
-}
-
+-static inline SimdDbl simdLoadDbl(const double *p) {
+- return _mm_loadu_pd(p);
+-}
+-
-static inline void simdStore(void *p, SimdInt x) {
- _mm_storeu_si128((SimdInt *)p, x);
-}
@@ -66,6 +76,10 @@ equivalents automatically
- _mm_storeu_si128((SimdInt *)p, x);
-}
-
+-static inline void simdStoreDbl(double *p, SimdDbl x) {
+- _mm_storeu_pd(p, x);
+-}
+-
-static inline SimdInt simdOr1(SimdInt x, SimdInt y) {
- return _mm_or_si128(x, y);
-}
@@ -75,6 +89,7 @@ equivalents automatically
-}
-
-const int simdLen = 4;
+-const int simdDblLen = 2;
-
-static inline SimdInt simdSet(int i3, int i2, int i1, int i0) {
- return _mm_set_epi32(i3, i2, i1, i0);
@@ -88,6 +103,10 @@ equivalents automatically
- i7, i6, i5, i4, i3, i2, i1, i0);
-}
-
+-static inline SimdDbl simdSetDbl(double i1, double i0) {
+- return _mm_set_pd(i1, i0);
+-}
+-
-static inline SimdInt simdFill(int x) {
- return _mm_set1_epi32(x);
-}
@@ -96,6 +115,10 @@ equivalents automatically
- return _mm_set1_epi8(x);
-}
-
+-static inline SimdDbl simdFillDbl(double x) {
+- return _mm_set1_pd(x);
+-}
+-
-static inline SimdInt simdGt(SimdInt x, SimdInt y) {
- return _mm_cmpgt_epi32(x, y);
-}
@@ -116,6 +139,10 @@ equivalents automatically
- return _mm_adds_epu8(x, y);
-}
-
+-static inline SimdDbl simdAddDbl(SimdDbl x, SimdDbl y) {
+- return _mm_add_pd(x, y);
+-}
+-
-static inline SimdInt simdSub(SimdInt x, SimdInt y) {
- return _mm_sub_epi32(x, y);
-}
@@ -124,6 +151,10 @@ equivalents automatically
- return _mm_sub_epi8(x, y);
-}
-
+-static inline SimdDbl simdMulDbl(SimdDbl x, SimdDbl y) {
+- return _mm_mul_pd(x, y);
+-}
+-
-static inline SimdInt simdQuadruple1(SimdInt x) {
- return _mm_slli_epi32(x, 2);
-}
@@ -148,6 +179,10 @@ equivalents automatically
- return _mm_extract_epi16(x, 0);
-}
-
+-static inline double simdHorizontalAddDbl(SimdDbl x) {
+- return _mm_cvtsd_f64(_mm_hadd_pd(x, x));
+-}
+-
-static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
- return _mm_shuffle_epi8(items, choices); // SSSE3
-}
@@ -157,6 +192,7 @@ equivalents automatically
-typedef int32x4_t SimdInt;
-typedef uint32x4_t SimdUint;
-typedef uint8x16_t SimdUint1;
+-typedef float64x2_t SimdDbl;
-
-const int simdBytes = 16;
-
@@ -168,6 +204,10 @@ equivalents automatically
- return vdupq_n_u8(0);
-}
-
+-static inline SimdDbl simdZeroDbl() {
+- return vdupq_n_f64(0);
+-}
+-
-static inline SimdUint1 simdOnes1() {
- return vdupq_n_u8(-1);
-}
@@ -180,6 +220,10 @@ equivalents automatically
- return vld1q_u8(p);
-}
-
+-static inline SimdDbl simdLoadDbl(const double *p) {
+- return vld1q_f64(p);
+-}
+-
-static inline void simdStore(int *p, SimdInt x) {
- vst1q_s32(p, x);
-}
@@ -188,6 +232,10 @@ equivalents automatically
- vst1q_u8(p, x);
-}
-
+-static inline void simdStoreDbl(double *p, SimdDbl x) {
+- vst1q_f64(p, x);
+-}
+-
-static inline SimdUint1 simdOr1(SimdUint1 x, SimdUint1 y) {
- return vorrq_u8(x, y);
-}
@@ -197,6 +245,7 @@ equivalents automatically
-}
-
-const int simdLen = 4;
+-const int simdDblLen = 2;
-
-static inline SimdInt simdSet(unsigned i3, unsigned i2,
- unsigned i1, unsigned i0) {
@@ -225,6 +274,10 @@ equivalents automatically
- return vcombine_u8(vcreate_u8(lo), vcreate_u8(hi));
-}
-
+-static inline SimdDbl simdSetDbl(double i1, double i0) {
+- return vcombine_f64(vdup_n_f64(i0), vdup_n_f64(i1));
+-}
+-
-static inline SimdInt simdFill(int x) {
- return vdupq_n_s32(x);
-}
@@ -233,6 +286,10 @@ equivalents automatically
- return vdupq_n_u8(x);
-}
-
+-static inline SimdDbl simdFillDbl(double x) {
+- return vdupq_n_f64(x);
+-}
+-
-static inline SimdUint simdGt(SimdInt x, SimdInt y) {
- return vcgtq_s32(x, y);
-}
@@ -253,6 +310,10 @@ equivalents automatically
- return vqaddq_u8(x, y);
-}
-
+-static inline SimdDbl simdAddDbl(SimdDbl x, SimdDbl y) {
+- return vaddq_f64(x, y);
+-}
+-
-static inline SimdInt simdSub(SimdInt x, SimdInt y) {
- return vsubq_s32(x, y);
-}
@@ -261,6 +322,10 @@ equivalents automatically
- return vsubq_u8(x, y);
-}
-
+-static inline SimdDbl simdMulDbl(SimdDbl x, SimdDbl y) {
+- return vmulq_f64(x, y);
+-}
+-
-static inline SimdUint1 simdQuadruple1(SimdUint1 x) {
- return vshlq_n_u8(x, 2);
-}
@@ -281,6 +346,10 @@ equivalents automatically
- return vminvq_u8(x);
-}
-
+-static inline double simdHorizontalAddDbl(SimdDbl x) {
+- return vaddvq_f64(x);
+-}
+-
-static inline SimdUint1 simdChoose1(SimdUint1 items, SimdUint1 choices) {
- return vqtbl1q_u8(items, choices);
-}
@@ -288,19 +357,29 @@ equivalents automatically
-#else
-
-typedef int SimdInt;
+-typedef double SimdDbl;
-const int simdBytes = 1;
-const int simdLen = 1;
+-const int simdDblLen = 1;
-static inline int simdZero() { return 0; }
+-static inline double simdZeroDbl() { return 0; }
-static inline int simdSet(int x) { return x; }
+-static inline double simdSetDbl(double x) { return x; }
-static inline int simdFill(int x) { return x; }
-static inline int simdLoad(const int *p) { return *p; }
+-static inline double simdLoadDbl(const double *p) { return *p; }
-static inline void simdStore(int *p, int x) { *p = x; }
+-static inline void simdStoreDbl(double *p, double x) { *p = x; }
+-static inline double simdFillDbl(double x) { return x; }
-static inline int simdGt(int x, int y) { return x > y; }
-static inline int simdAdd(int x, int y) { return x + y; }
+-static inline double simdAddDbl(double x, double y) { return x + y; }
-static inline int simdSub(int x, int y) { return x - y; }
+-static inline double simdMulDbl(double x, double y) { return x * y; }
-static inline int simdMax(int x, int y) { return x > y ? x : y; }
-static inline int simdBlend(int x, int y, int mask) { return mask ? y : x; }
-static inline int simdHorizontalMax(int a) { return a; }
+-static inline double simdHorizontalAddDbl(double x) { return x; }
-
-#endif
-
@@ -309,7 +388,7 @@ equivalents automatically
#endif
--- a/src/GappedXdropAligner.cc
+++ b/src/GappedXdropAligner.cc
-@@ -140,17 +140,13 @@ int GappedXdropAligner::align(const ucha
+@@ -140,17 +140,13 @@
if (isAffine) {
for (int i = 0; i < numCells; i += simdLen) {
SimdInt s = simdSet(
@@ -329,7 +408,7 @@ equivalents automatically
SimdInt y = simdSub(simdLoad(y1+i), mDelGrowCost);
--- a/src/GappedXdropAlignerPssm.cc
+++ b/src/GappedXdropAlignerPssm.cc
-@@ -91,17 +91,13 @@ int GappedXdropAligner::alignPssm(const
+@@ -91,17 +91,13 @@
if (isAffine) {
for (int i = 0; i < numCells; i += simdLen) {
SimdInt s = simdSet(
@@ -363,7 +442,7 @@ equivalents automatically
CXXFLAGS += -std=c++11
CXXFLAGS += -pthread -DHAS_CXX_THREAD
# -fomit-frame-pointer ?
-@@ -56,11 +55,12 @@ split/last-split.o
+@@ -56,11 +55,12 @@
PPOBJ = last-pair-probs.o last-pair-probs-main.o
MBOBJ = last-merge-batches.o
@@ -380,7 +459,7 @@ equivalents automatically
indexObj5 = $(indexObj4:.o=.o5)
alignObj5 = $(alignObj4:.o=.o5)
-@@ -74,45 +74,45 @@ all: $(ALL)
+@@ -74,45 +74,45 @@
last8: $(LAST8)
indexAllObj4 = $(indexObj0) $(indexObj4)
@@ -448,7 +527,7 @@ equivalents automatically
//#include <iostream> // for debugging
namespace cbrc {
-@@ -43,12 +41,10 @@ int GappedXdropAligner::alignDna(const u
+@@ -43,12 +41,10 @@
const SimdUint1 scorer4x4 =
simdSet1(
@@ -461,7 +540,7 @@ equivalents automatically
scorer[3][3], scorer[3][2], scorer[3][1], scorer[3][0],
scorer[2][3], scorer[2][2], scorer[2][1], scorer[2][0],
scorer[1][3], scorer[1][2], scorer[1][1], scorer[1][0],
-@@ -126,7 +122,6 @@ int GappedXdropAligner::alignDna(const u
+@@ -126,7 +122,6 @@
for (int i = 0; i < numCells; i += simdBytes) {
SimdUint1 s = simdSet1(
@@ -469,7 +548,7 @@ equivalents automatically
scorer[s1[31]][s2[31]],
scorer[s1[30]][s2[30]],
scorer[s1[29]][s2[29]],
-@@ -143,7 +138,6 @@ int GappedXdropAligner::alignDna(const u
+@@ -143,7 +138,6 @@
scorer[s1[18]][s2[18]],
scorer[s1[17]][s2[17]],
scorer[s1[16]][s2[16]],
@@ -477,7 +556,7 @@ equivalents automatically
scorer[s1[15]][s2[15]],
scorer[s1[14]][s2[14]],
scorer[s1[13]][s2[13]],
-@@ -275,5 +269,3 @@ bool GappedXdropAligner::getNextChunkDna
+@@ -275,5 +269,3 @@
}
}
@@ -485,7 +564,7 @@ equivalents automatically
-#endif
--- a/src/Alignment.cc
+++ b/src/Alignment.cc
-@@ -365,12 +365,10 @@ void Alignment::extend( std::vector< Seg
+@@ -365,12 +365,10 @@
del.openCost, del.growCost,
ins.openCost, ins.growCost,
gap.pairCost, gap.isAffine, maxDrop, smMax)
@@ -498,7 +577,7 @@ equivalents automatically
: aligner.align(seq1, seq2, isForward, globality, sm,
del.openCost, del.growCost,
ins.openCost, ins.growCost,
-@@ -387,14 +385,12 @@ void Alignment::extend( std::vector< Seg
+@@ -387,14 +385,12 @@
while( greedyAligner.getNextChunk( end1, end2, size ) )
chunks.push_back( SegmentPair( end1 - size, end2 - size, size ) );
}
@@ -515,7 +594,7 @@ equivalents automatically
del.openCost, del.growCost,
--- a/src/GappedXdropAligner.hh
+++ b/src/GappedXdropAligner.hh
-@@ -352,7 +352,6 @@ class GappedXdropAligner {
+@@ -352,7 +352,6 @@
void initFrame();
// Everything below here is for alignDna & getNextChunkDna
@@ -523,7 +602,7 @@ equivalents automatically
std::vector<TinyScore> xTinyScores;
std::vector<TinyScore> yTinyScores;
std::vector<TinyScore> zTinyScores;
-@@ -402,7 +401,6 @@ class GappedXdropAligner {
+@@ -402,7 +401,6 @@
while (*x2 != target) ++x2;
bestSeq1position = x2 - x2beg + seq1beg;
}
@@ -531,3 +610,33 @@ equivalents automatically
};
}
+--- a/src/tantan.cc
++++ b/src/tantan.cc
+@@ -324,13 +324,9 @@
+ int i = 0;
+ for (; i <= maxOffset - simdDblLen; i += simdDblLen) {
+ SimdDbl rV = simdSetDbl(
+-#if defined __SSE4_1__ || defined __ARM_NEON
+-#ifdef __AVX2__
+ lrRow[sp[-i-4]],
+ lrRow[sp[-i-3]],
+-#endif
+ lrRow[sp[-i-2]],
+-#endif
+ lrRow[sp[-i-1]]);
+ SimdDbl fV = simdLoadDbl(fp+i);
+ sV = simdAddDbl(sV, fV);
+@@ -368,13 +364,9 @@
+ int i = 0;
+ for (; i <= maxOffset - simdDblLen; i += simdDblLen) {
+ SimdDbl rV = simdSetDbl(
+-#if defined __SSE4_1__ || defined __ARM_NEON
+-#ifdef __AVX2__
+ lrRow[sp[-i-4]],
+ lrRow[sp[-i-3]],
+-#endif
+ lrRow[sp[-i-2]],
+-#endif
+ lrRow[sp[-i-1]]);
+ SimdDbl fV = simdMulDbl(simdLoadDbl(fp+i), rV);
+ sV = simdAddDbl(sV, simdMulDbl(simdLoadDbl(b2f+i), fV));
=====================================
doc/FAQ.rst
=====================================
@@ -1,6 +1,26 @@
LAST FAQ
========
+:Q: Why does LAST sometimes miss strong alignments?
+
+:A: This is because it avoids getting huge numbers of repetitive
+ alignments, by just finding a few strongest matches for each part
+ of each query sequence. To find more repetitive matches, increase
+ the ``lastal -m`` parameter, e.g. ``-m100``.
+
+..
+
+:Q: Why does LAST sometimes show two separate alignments, and
+ sometimes one merged alignment, between the same sequences?
+
+:A: This is because LAST forbids highly dissimilar regions inside
+ alignments, but the maximum-allowed dissimilarity depends on the
+ alignment score / E-value threshold (which depends on the database
+ size). For more details, please see the discussion of "X-drop" in
+ `Parameters for accurate genome alignment`_.
+
+..
+
:Q: Does it matter which sequence is used as the "reference" (given to
lastdb) and which is used as the "query" (given to lastal)?
@@ -43,15 +63,6 @@ LAST FAQ
..
-:Q: I'd like to compare my queries to a database of known proteins.
- Where can I get a database of known proteins?
-
-:A: You could try UniRef90 or UniRef50
- (http://www.uniprot.org/help/uniref), which have reduced
- redundancy.
-
-..
-
:Q: How does LAST get the sequence names? How can I get nice, short,
unique names?
@@ -88,3 +99,5 @@ RAQ (Rarely Asked Questions)
command with::
numactl --interleave=all
+
+.. _Parameters for accurate genome alignment: https://doi.org/10.1186/1471-2105-11-80
=====================================
doc/bisulfite.rst
=====================================
@@ -4,8 +4,7 @@ Aligning bisulfite-converted DNA reads to a genome
The easy way
------------
-Use `Bisulfighter <http://epigenome.cbrc.jp/bisulfighter>`_, which
-wraps LAST.
+Use Bisulfighter_, which wraps LAST.
The hard way
------------
@@ -81,3 +80,5 @@ This assumes that reads1.fastq are all from the converted strand
reverse-complement (i.e. they have G->A conversions). It requires GNU
parallel to be installed. You are encouraged to customize this
script.
+
+.. _Bisulfighter: https://github.com/yutaka-saito/Bisulfighter
=====================================
doc/last-papers.rst
=====================================
@@ -127,7 +127,7 @@ research to society.
15. `Improved DNA-versus-protein homology search for protein fossils`__.
Yao Y, Frith MC.
- __ https://doi.org/10.1101/2021.01.25.428050
+ __ https://doi.org/10.1007/978-3-030-74432-8_11
Describes "new-style" DNA-versus-protein search with
``last-train --codon``.
=====================================
doc/last-split.rst
=====================================
@@ -1,14 +1,22 @@
last-split
==========
-This program finds "split alignments" (typically for DNA) or "spliced
+last-split finds "split alignments" (typically for DNA) or "spliced
alignments" (typically for RNA).
-It reads candidate alignments of query sequences to a genome, and
-looks for a unique best alignment for each part of each query. It
-allows different parts of one query to match different parts of the
-genome. This is useful for DNA queries that cross rearrangement
-breakpoints, or RNA queries that cross splice junctions.
+It reads candidate alignments of query sequences to a genome, and cuts
+from them a unique best alignment for each part of each query. This
+is useful for DNA queries that cross rearrangement breakpoints, or RNA
+queries that cross splice junctions.
+
+For a detailed explanation of what last-split does, please see `A
+survey of localized sequence rearrangements in human DNA
+<https://doi.org/10.1093/nar/gkx1266>`_ (update in `A pipeline for
+complete characterization of complex germline rearrangements from long
+DNA reads <https://doi.org/10.1186/s13073-020-00762-1>`_). The
+algorithm, and application to whole genomes, is in `Split-alignment of
+genomes finds orthologies more accurately
+<https://doi.org/10.1186/s13059-015-0670-9>`_.
Examples
--------
@@ -34,12 +42,13 @@ tells it where the splice signals are (GT, AG, etc)::
lastal -p train.out -D10 db q.fastq | last-split -g db > out.maf
-This will favour splices starting at GT (and to a lesser extent GC and
-AT), and ending at AG (and to a lesser extent AC). However, it allows
-splices starting and ending anywhere. It also favours splices with
-introns of typical length, specified by a log-normal distribution
-(i.e. cis-splices). However, it allows arbitrary trans-splices
-between any two places in the genome.
+This will favor splices starting at GT (and to a lesser extent GC and
+AT), and ending at AG (and to a lesser extent AC). The output shows
+the donor (``don``) and acceptor (``acc``) dinucleotides.
+
+It also favors splices with introns of typical length, specified by a
+log-normal distribution (cis-splices). However, it allows arbitrary
+trans-splices between any two places in the genome.
``-D10`` sets a very loose significance threshold, so that we can find
very short parts of a spliced alignment (e.g. short exons). Note that
@@ -148,19 +157,20 @@ Faster spliced alignment
~~~~~~~~~~~~~~~~~~~~~~~~
Spliced alignment can be slow. It can be sped up, at a small cost in
-accuracy, by not favouring cis-splices::
+accuracy, by not favoring cis-splices::
lastal -p train.out -D10 db q.fastq | last-split -c0 -t0.004 -g db > out.maf
The ``-c0`` turns off cis-splicing, and the ``-t0.004`` specifies a
-higher probability of trans-splicing.
+higher probability of "trans-splicing" (which includes cis-splicing,
+just doesn't favor it).
"Spliced" alignment of DNA reads to a genome
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
If we do not wish to allow arbitrarily large unaligned parts in the
middle of the query, we can do "spliced" alignment without considering
-splice signals or favouring cis-splices::
+splice signals or favoring cis-splices::
lastal -p train.out db q.fastq | last-split -c0 > out.maf
@@ -193,12 +203,33 @@ Options
determines whether forward and/or reverse-complement splice
signals are used.
- If you use ``-d2``, the output will have an extra "sense"
+ If you use ``-d2``, the output will have an extra ``sense``
field, indicating the log-odds that the query is
sense-stranded::
log2[ prob(sense) / prob(antisense) ]
+ The donor and acceptor annotations also indicate strandedness.
+ This order means that the query sequence is from the forward
+ strand of a spliced RNA::
+
+ don
+ acc don
+ acc don
+ acc
+
+ And this order means it is from the reverse strand::
+
+ acc
+ don acc
+ don acc
+ don
+
+ It's possible for ``don`` and ``acc`` to conflict with
+ ``sense``. That happens if one orientation is overall more
+ likely (indicated by ``sense``), but any one alignment with
+ that orientation is not the most likely.
+
-c, --cis=PROB
Do spliced alignment, and set the average probability per
base of cis-splicing. The default value roughly fits human
@@ -260,10 +291,10 @@ Details
(of the kind produced by lastal) describing the alignment score
parameters.
-* The program reads one batch of alignments at a time (by looking for
- lines starting with "# batch"). If the batches are huge
- (e.g. because there are no lines starting with "# batch"), it might
- need too much memory.
+* The input must not mix alignments of different query sequences. In
+ other words, all the alignments of one query must be next to each
+ other. If you use ``-r``/``--reverse``, however, there is no such
+ requirement, and the whole input gets read into memory.
* lastal can optionally write "p" lines, indicating the probability
that each base is misaligned due to wrong gap placement.
@@ -285,8 +316,8 @@ last-split5
-----------
last-split5 is almost identical to last-split. The only difference is
-the -g option: last-split can only read the output of lastdb, whereas
-last-split5 can only read the output of lastdb5_.
+the ``-g`` option: last-split can only read the output of lastdb,
+whereas last-split5 can only read the output of lastdb5_.
Limitations
-----------
=====================================
doc/lastal.rst
=====================================
@@ -318,7 +318,7 @@ Miscellaneous options
single sequence exceeds this amount, however, it is not split.
You can use suffixes K, M, and G to specify KibiBytes,
MebiBytes, and GibiBytes. This option has no effect on the
- results (apart from their order).
+ results.
If the reference was split into volumes by lastdb_, then each
volume will be read into memory once per query batch.
=====================================
examples/last-bisulfite.sh
=====================================
@@ -30,8 +30,8 @@ trap 'rm -f $tmp.*' EXIT
# Convert C to t, and all other letters to uppercase:
perl -pe 'y/Cca-z/ttA-Z/ if $. % 4 == 2' "$@" > "$tmp".q
-lastal -pBISF -s1 -Q1 -D1000 "$my_f" "$tmp".q > "$tmp".f
-lastal -pBISR -s0 -Q1 -D1000 "$my_r" "$tmp".q > "$tmp".r
+lastal -pBISF -s1 -Q1 -D1000 -i1 "$my_f" "$tmp".q > "$tmp".f
+lastal -pBISR -s0 -Q1 -D1000 -i1 "$my_r" "$tmp".q > "$tmp".r
last-merge-batches "$tmp".f "$tmp".r | last-split -m0.1 -fMAF+ |
perl -F'(\s+)' -ane '$F[12] =~ y/ta/CG/ if /^s/ and $s++ % 2; print @F'
=====================================
src/lastal.cc
=====================================
@@ -93,6 +93,7 @@ namespace {
sequenceFormat::Enum referenceFormat = sequenceFormat::fasta;
int minScoreGapless;
int isCaseSensitiveSeeds = -1; // initialize it to an "error" value
+ unsigned numOfVolumes = -1;
unsigned numOfIndexes = 1; // assume this value, if unspecified
}
@@ -341,11 +342,10 @@ static void calculateScoreStatistics(const std::string& matrixName,
}
// Read the .prj file for the whole database
-void readOuterPrj( const std::string& fileName, unsigned& volumes,
- size_t& refMinimizerWindow, size_t& minSeedLimit,
- bool& isKeepRefLowercase, int& refTantanSetting,
- countT& refSequences, countT& refLetters,
- countT& refMaxSeqLen ){
+void readOuterPrj(const std::string &fileName, size_t &refMinimizerWindow,
+ size_t &minSeedLimit, bool &isKeepRefLowercase,
+ int &refTantanSetting, countT &refSequences,
+ countT &refLetters, countT &refMaxSeqLen) {
std::ifstream f( fileName.c_str() );
if( !f ) ERR( "can't open file: " + fileName );
unsigned version = 0;
@@ -371,7 +371,7 @@ void readOuterPrj( const std::string& fileName, unsigned& volumes,
if( word == "masklowercase" ) iss >> isCaseSensitiveSeeds;
if( word == "sequenceformat" ) iss >> referenceFormat;
if( word == "minimizerwindow" ) iss >> refMinimizerWindow;
- if( word == "volumes" ) iss >> volumes;
+ if( word == "volumes" ) iss >> numOfVolumes;
if( word == "numofindexes" ) iss >> numOfIndexes;
if( word == "integersize" ) iss >> fileBitsPerInt;
}
@@ -419,15 +419,15 @@ void readInnerPrj( const std::string& fileName,
}
// Write match counts for each query sequence
-void writeCounts( std::ostream& out ){
+void writeCounts() {
for( indexT i = 0; i < matchCounts.size(); ++i ){
- out << query.seqName(i) << '\n';
+ std::cout << query.seqName(i) << '\n';
for( size_t j = args.minHitDepth; j < matchCounts[i].size(); ++j ){
- out << j << '\t' << matchCounts[i][j] << '\n';
+ std::cout << j << '\t' << matchCounts[i][j] << '\n';
}
- out << '\n'; // blank line afterwards
+ std::cout << '\n'; // blank line afterwards
}
}
@@ -544,7 +544,7 @@ struct Dispatcher{
static bool isCollatedAlignments() {
return args.outputFormat == 'b' || args.outputFormat == 'B' ||
- args.cullingLimitForFinalAlignments + 1;
+ args.cullingLimitForFinalAlignments + 1 || numOfVolumes > 1;
}
static void printAndDelete(char *text) {
@@ -913,11 +913,6 @@ static void printAndClear(std::vector<AlignmentText> &textAlns) {
textAlns.clear();
}
-static void printAndClearAll() {
- for (size_t i = 0; i < aligners.size(); ++i)
- printAndClear(aligners[i].textAlns);
-}
-
void makeQualityPssm( LastAligner& aligner,
size_t queryNum, const SubstitutionMatrices &matrices,
const uchar* querySeq, bool isMask ){
@@ -1041,7 +1036,7 @@ void scan(LastAligner& aligner, size_t queryNum,
}
}
- if( !isCollatedAlignments() ) gappedAlns.sort(); // sort by score
+ if (!isCollatedAlignments()) gappedAlns.sort(); // sort by score
alignFinish(aligner, gappedAlns, queryNum, matrices, frameSize, dis3);
}
@@ -1130,20 +1125,17 @@ static void alignOneQuery(LastAligner &aligner, size_t finalCullingLimit,
args.isQueryStrandMatrix ? revMatrices : fwdMatrices);
}
-static void alignSomeQueries(size_t chunkNum,
- unsigned volume, unsigned volumeCount) {
+static void alignSomeQueries(size_t chunkNum, unsigned volume) {
size_t numOfChunks = aligners.size();
LastAligner &aligner = aligners[chunkNum];
std::vector<AlignmentText> &textAlns = aligner.textAlns;
size_t beg = firstSequenceInChunk(query, numOfChunks, chunkNum);
size_t end = firstSequenceInChunk(query, numOfChunks, chunkNum + 1);
- bool isMultiVolume = (volumeCount > 1);
+ bool isMultiVolume = (numOfVolumes > 1);
bool isFirstVolume = (volume == 0);
- bool isFinalVolume = (volume + 1 == volumeCount);
bool isFirstThread = (chunkNum == 0);
- bool isSort = isCollatedAlignments();
- bool isSortPerQuery = (isSort && !isMultiVolume);
- bool isPrintPerQuery = (isFirstThread && !(isSort && isMultiVolume));
+ bool isSortPerQuery = (isCollatedAlignments() && !isMultiVolume);
+ bool isPrintPerQuery = (isFirstThread && !isMultiVolume);
size_t finalCullingLimit = args.cullingLimitForFinalAlignments ?
args.cullingLimitForFinalAlignments : isMultiVolume;
for (size_t i = beg; i < end; ++i) {
@@ -1152,27 +1144,27 @@ static void alignSomeQueries(size_t chunkNum,
if (isSortPerQuery) sort(textAlns.begin() + oldNumOfAlns, textAlns.end());
if (isPrintPerQuery) printAndClear(textAlns);
}
- if (isFinalVolume && isMultiVolume) {
+ if (isMultiVolume && volume + 1 == numOfVolumes) {
cullFinalAlignments(textAlns, 0, args.cullingLimitForFinalAlignments);
- if (isSort) sort(textAlns.begin(), textAlns.end());
- if (isFirstThread) printAndClear(textAlns);
+ sort(textAlns.begin(), textAlns.end());
}
}
-static void scanOneVolume(unsigned volume, unsigned volumeCount) {
-#ifdef HAS_CXX_THREADS
- size_t numOfChunks = aligners.size();
- std::vector<std::thread> threads(numOfChunks - 1);
- for (size_t i = 1; i < numOfChunks; ++i)
- threads[i - 1] = std::thread(alignSomeQueries, i, volume, volumeCount);
- // Exceptions from threads are not handled nicely, but I don't
- // think it matters much.
-#endif
- alignSomeQueries(0, volume, volumeCount);
+static void scanOneVolume(unsigned volume, unsigned numOfThreadsLeft) {
+ if (numOfThreadsLeft > 1) {
#ifdef HAS_CXX_THREADS
- for (size_t i = 1; i < numOfChunks; ++i)
- threads[i - 1].join();
+ std::thread t(scanOneVolume, volume, numOfThreadsLeft - 1);
+ // Exceptions from threads are not handled nicely, but I don't
+ // think it matters much.
+ alignSomeQueries(numOfThreadsLeft - 1, volume);
+ t.join();
#endif
+ } else {
+ alignSomeQueries(0, volume);
+ }
+ if (volume + 1 == numOfVolumes) {
+ printAndClear(aligners[numOfThreadsLeft - 1].textAlns);
+ }
}
void readIndex( const std::string& baseName, indexT seqCount ) {
@@ -1242,23 +1234,18 @@ void readVolume( unsigned volumeNumber ){
}
// Scan one batch of query sequences against all database volumes
-void scanAllVolumes( unsigned volumes, std::ostream& out ){
+void scanAllVolumes() {
if( args.outputType == 0 ){
matchCounts.clear();
matchCounts.resize( query.finishedSequences() );
}
- if( volumes+1 == 0 ) volumes = 1;
- bool isMultiVolume = (volumes > 1);
-
- for( unsigned i = 0; i < volumes; ++i ){
- if( text.unfinishedSize() == 0 || isMultiVolume ) readVolume( i );
- scanOneVolume( i, volumes );
- if( !isCollatedAlignments() ) printAndClearAll();
+ for (unsigned i = 0; i < numOfVolumes; ++i) {
+ if (text.unfinishedSize() == 0 || numOfVolumes > 1) readVolume(i);
+ scanOneVolume(i, aligners.size());
}
- if( args.outputType == 0 ) writeCounts( out );
- printAndClearAll();
+ if (args.outputType == 0) writeCounts();
}
void writeHeader( countT refSequences, countT refLetters, std::ostream& out ){
@@ -1311,7 +1298,6 @@ void lastal( int argc, char** argv ){
args.fromArgs( argc, argv );
args.resetCumulativeOptions(); // because we will do fromArgs again
- unsigned volumes = unsigned(-1);
size_t refMinimizerWindow = 1; // assume this value, if not specified
size_t minSeedLimit = 0;
countT refSequences = -1;
@@ -1319,10 +1305,9 @@ void lastal( int argc, char** argv ){
countT refMaxSeqLen = -1;
bool isKeepRefLowercase = true;
int refTantanSetting = 0;
- readOuterPrj( args.lastdbName + ".prj", volumes,
- refMinimizerWindow, minSeedLimit,
- isKeepRefLowercase, refTantanSetting,
- refSequences, refLetters, refMaxSeqLen );
+ readOuterPrj(args.lastdbName + ".prj",
+ refMinimizerWindow, minSeedLimit, isKeepRefLowercase,
+ refTantanSetting, refSequences, refLetters, refMaxSeqLen);
bool isDna = (alph.letters == alph.dna);
bool isProtein = alph.isProtein();
@@ -1354,7 +1339,7 @@ void lastal( int argc, char** argv ){
aligners.resize( decideNumberOfThreads( args.numOfThreads,
args.programName, args.verbosity ) );
- bool isMultiVolume = (volumes+1 > 0 && volumes > 1);
+ bool isMultiVolume = (numOfVolumes + 1 > 0 && numOfVolumes > 1);
args.setDefaultsFromAlphabet( isDna, isProtein,
isKeepRefLowercase, refTantanSetting,
isCaseSensitiveSeeds, isMultiVolume,
@@ -1412,11 +1397,12 @@ void lastal( int argc, char** argv ){
queryAlph.tr(query.seqWriter(), query.seqWriter() + query.seqBeg(0));
- if( volumes+1 == 0 ) readIndex( args.lastdbName, refSequences );
+ if (numOfVolumes + 1 == 0) {
+ readIndex(args.lastdbName, refSequences);
+ numOfVolumes = 1;
+ }
- std::ostream& out = std::cout;
- writeHeader( refSequences, refLetters, out );
- out.precision(3); // print non-integers more compactly
+ writeHeader(refSequences, refLetters, std::cout);
countT queryBatchCount = 0;
countT sequenceCount = 0;
indexT maxSeqLen = args.batchSize;
@@ -1437,24 +1423,24 @@ void lastal( int argc, char** argv ){
++sequenceCount;
} else {
// this enables downstream parsers to read one batch at a time:
- out << "# batch " << queryBatchCount++ << "\n";
- scanAllVolumes( volumes, out );
+ std::cout << "# batch " << queryBatchCount++ << "\n";
+ scanAllVolumes();
query.reinitForAppending();
}
}
}
if( query.finishedSequences() > 0 ){
- out << "# batch " << queryBatchCount << "\n";
- scanAllVolumes( volumes, out );
+ std::cout << "# batch " << queryBatchCount << "\n";
+ scanAllVolumes();
}
countT numOfNormalLetters = 0;
for (size_t i = 0; i < aligners.size(); ++i) {
numOfNormalLetters += aligners[i].numOfNormalLetters;
}
- out << "# Query sequences=" << sequenceCount
- << " normal letters=" << numOfNormalLetters << "\n";
+ std::cout << "# 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: 1268) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1282) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
src/mcf_simd.hh
=====================================
@@ -18,6 +18,7 @@ namespace mcf {
typedef __m256i SimdInt;
typedef __m256i SimdUint1;
+typedef __m256d SimdDbl;
const int simdBytes = 32;
@@ -29,6 +30,10 @@ static inline SimdInt simdZero1() {
return _mm256_setzero_si256();
}
+static inline SimdDbl simdZeroDbl() {
+ return _mm256_setzero_pd();
+}
+
static inline SimdInt simdOnes1() {
return _mm256_set1_epi32(-1);
}
@@ -41,6 +46,10 @@ static inline SimdInt simdLoad1(const void *p) {
return _mm256_loadu_si256((const SimdInt *)p);
}
+static inline SimdDbl simdLoadDbl(const double *p) {
+ return _mm256_loadu_pd(p);
+}
+
static inline void simdStore(void *p, SimdInt x) {
_mm256_storeu_si256((SimdInt *)p, x);
}
@@ -49,6 +58,10 @@ static inline void simdStore1(void *p, SimdInt x) {
_mm256_storeu_si256((SimdInt *)p, x);
}
+static inline void simdStoreDbl(double *p, SimdDbl x) {
+ _mm256_storeu_pd(p, x);
+}
+
static inline SimdInt simdOr1(SimdInt x, SimdInt y) {
return _mm256_or_si256(x, y);
}
@@ -58,6 +71,7 @@ static inline SimdInt simdBlend(SimdInt x, SimdInt y, SimdInt mask) {
}
const int simdLen = 8;
+const int simdDblLen = 4;
static inline SimdInt simdSet(int i7, int i6, int i5, int i4,
int i3, int i2, int i1, int i0) {
@@ -78,6 +92,10 @@ static inline SimdInt simdSet1(char jF, char jE, char jD, char jC,
i7, i6, i5, i4, i3, i2, i1, i0);
}
+static inline SimdDbl simdSetDbl(double i3, double i2, double i1, double i0) {
+ return _mm256_set_pd(i3, i2, i1, i0);
+}
+
static inline SimdInt simdFill(int x) {
return _mm256_set1_epi32(x);
}
@@ -86,6 +104,10 @@ static inline SimdInt simdFill1(char x) {
return _mm256_set1_epi8(x);
}
+static inline SimdDbl simdFillDbl(double x) {
+ return _mm256_set1_pd(x);
+}
+
static inline SimdInt simdGt(SimdInt x, SimdInt y) {
return _mm256_cmpgt_epi32(x, y);
}
@@ -106,6 +128,10 @@ static inline SimdInt simdAdds1(SimdInt x, SimdInt y) {
return _mm256_adds_epu8(x, y);
}
+static inline SimdDbl simdAddDbl(SimdDbl x, SimdDbl y) {
+ return _mm256_add_pd(x, y);
+}
+
static inline SimdInt simdSub(SimdInt x, SimdInt y) {
return _mm256_sub_epi32(x, y);
}
@@ -114,6 +140,10 @@ static inline SimdInt simdSub1(SimdInt x, SimdInt y) {
return _mm256_sub_epi8(x, y);
}
+static inline SimdDbl simdMulDbl(SimdDbl x, SimdDbl y) {
+ return _mm256_mul_pd(x, y);
+}
+
static inline SimdInt simdQuadruple1(SimdInt x) {
return _mm256_slli_epi32(x, 2);
}
@@ -142,6 +172,12 @@ static inline int simdHorizontalMin1(SimdInt x) {
return _mm_extract_epi16(z, 0);
}
+static inline double simdHorizontalAddDbl(SimdDbl x) {
+ __m128d z = _mm256_castpd256_pd128(x);
+ z = _mm_add_pd(z, _mm256_extractf128_pd(x, 1));
+ return _mm_cvtsd_f64(_mm_hadd_pd(z, z));
+}
+
static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
return _mm256_shuffle_epi8(items, choices);
}
@@ -150,6 +186,7 @@ static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
typedef __m128i SimdInt;
typedef __m128i SimdUint1;
+typedef __m128d SimdDbl;
const int simdBytes = 16;
@@ -161,6 +198,10 @@ static inline SimdInt simdZero1() {
return _mm_setzero_si128();
}
+static inline SimdDbl simdZeroDbl() {
+ return _mm_setzero_pd();
+}
+
static inline SimdInt simdOnes1() {
return _mm_set1_epi32(-1);
}
@@ -173,6 +214,10 @@ static inline SimdInt simdLoad1(const void *p) {
return _mm_loadu_si128((const SimdInt *)p);
}
+static inline SimdDbl simdLoadDbl(const double *p) {
+ return _mm_loadu_pd(p);
+}
+
static inline void simdStore(void *p, SimdInt x) {
_mm_storeu_si128((SimdInt *)p, x);
}
@@ -181,6 +226,10 @@ static inline void simdStore1(void *p, SimdInt x) {
_mm_storeu_si128((SimdInt *)p, x);
}
+static inline void simdStoreDbl(double *p, SimdDbl x) {
+ _mm_storeu_pd(p, x);
+}
+
static inline SimdInt simdOr1(SimdInt x, SimdInt y) {
return _mm_or_si128(x, y);
}
@@ -190,6 +239,7 @@ static inline SimdInt simdBlend(SimdInt x, SimdInt y, SimdInt mask) {
}
const int simdLen = 4;
+const int simdDblLen = 2;
static inline SimdInt simdSet(int i3, int i2, int i1, int i0) {
return _mm_set_epi32(i3, i2, i1, i0);
@@ -203,6 +253,10 @@ static inline SimdInt simdSet1(char iF, char iE, char iD, char iC,
i7, i6, i5, i4, i3, i2, i1, i0);
}
+static inline SimdDbl simdSetDbl(double i1, double i0) {
+ return _mm_set_pd(i1, i0);
+}
+
static inline SimdInt simdFill(int x) {
return _mm_set1_epi32(x);
}
@@ -211,6 +265,10 @@ static inline SimdInt simdFill1(char x) {
return _mm_set1_epi8(x);
}
+static inline SimdDbl simdFillDbl(double x) {
+ return _mm_set1_pd(x);
+}
+
static inline SimdInt simdGt(SimdInt x, SimdInt y) {
return _mm_cmpgt_epi32(x, y);
}
@@ -231,6 +289,10 @@ static inline SimdInt simdAdds1(SimdInt x, SimdInt y) {
return _mm_adds_epu8(x, y);
}
+static inline SimdDbl simdAddDbl(SimdDbl x, SimdDbl y) {
+ return _mm_add_pd(x, y);
+}
+
static inline SimdInt simdSub(SimdInt x, SimdInt y) {
return _mm_sub_epi32(x, y);
}
@@ -239,6 +301,10 @@ static inline SimdInt simdSub1(SimdInt x, SimdInt y) {
return _mm_sub_epi8(x, y);
}
+static inline SimdDbl simdMulDbl(SimdDbl x, SimdDbl y) {
+ return _mm_mul_pd(x, y);
+}
+
static inline SimdInt simdQuadruple1(SimdInt x) {
return _mm_slli_epi32(x, 2);
}
@@ -263,6 +329,10 @@ static inline int simdHorizontalMin1(SimdInt x) {
return _mm_extract_epi16(x, 0);
}
+static inline double simdHorizontalAddDbl(SimdDbl x) {
+ return _mm_cvtsd_f64(_mm_hadd_pd(x, x));
+}
+
static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
return _mm_shuffle_epi8(items, choices); // SSSE3
}
@@ -272,6 +342,7 @@ static inline SimdInt simdChoose1(SimdInt items, SimdInt choices) {
typedef int32x4_t SimdInt;
typedef uint32x4_t SimdUint;
typedef uint8x16_t SimdUint1;
+typedef float64x2_t SimdDbl;
const int simdBytes = 16;
@@ -283,6 +354,10 @@ static inline SimdUint1 simdZero1() {
return vdupq_n_u8(0);
}
+static inline SimdDbl simdZeroDbl() {
+ return vdupq_n_f64(0);
+}
+
static inline SimdUint1 simdOnes1() {
return vdupq_n_u8(-1);
}
@@ -295,6 +370,10 @@ static inline SimdUint1 simdLoad1(const unsigned char *p) {
return vld1q_u8(p);
}
+static inline SimdDbl simdLoadDbl(const double *p) {
+ return vld1q_f64(p);
+}
+
static inline void simdStore(int *p, SimdInt x) {
vst1q_s32(p, x);
}
@@ -303,6 +382,10 @@ static inline void simdStore1(unsigned char *p, SimdUint1 x) {
vst1q_u8(p, x);
}
+static inline void simdStoreDbl(double *p, SimdDbl x) {
+ vst1q_f64(p, x);
+}
+
static inline SimdUint1 simdOr1(SimdUint1 x, SimdUint1 y) {
return vorrq_u8(x, y);
}
@@ -312,6 +395,7 @@ static inline SimdInt simdBlend(SimdInt x, SimdInt y, SimdUint mask) {
}
const int simdLen = 4;
+const int simdDblLen = 2;
static inline SimdInt simdSet(unsigned i3, unsigned i2,
unsigned i1, unsigned i0) {
@@ -340,6 +424,10 @@ static inline SimdUint1 simdSet1(unsigned char iF, unsigned char iE,
return vcombine_u8(vcreate_u8(lo), vcreate_u8(hi));
}
+static inline SimdDbl simdSetDbl(double i1, double i0) {
+ return vcombine_f64(vdup_n_f64(i0), vdup_n_f64(i1));
+}
+
static inline SimdInt simdFill(int x) {
return vdupq_n_s32(x);
}
@@ -348,6 +436,10 @@ static inline SimdUint1 simdFill1(unsigned char x) {
return vdupq_n_u8(x);
}
+static inline SimdDbl simdFillDbl(double x) {
+ return vdupq_n_f64(x);
+}
+
static inline SimdUint simdGt(SimdInt x, SimdInt y) {
return vcgtq_s32(x, y);
}
@@ -368,6 +460,10 @@ static inline SimdUint1 simdAdds1(SimdUint1 x, SimdUint1 y) {
return vqaddq_u8(x, y);
}
+static inline SimdDbl simdAddDbl(SimdDbl x, SimdDbl y) {
+ return vaddq_f64(x, y);
+}
+
static inline SimdInt simdSub(SimdInt x, SimdInt y) {
return vsubq_s32(x, y);
}
@@ -376,6 +472,10 @@ static inline SimdUint1 simdSub1(SimdUint1 x, SimdUint1 y) {
return vsubq_u8(x, y);
}
+static inline SimdDbl simdMulDbl(SimdDbl x, SimdDbl y) {
+ return vmulq_f64(x, y);
+}
+
static inline SimdUint1 simdQuadruple1(SimdUint1 x) {
return vshlq_n_u8(x, 2);
}
@@ -396,6 +496,10 @@ static inline int simdHorizontalMin1(SimdUint1 x) {
return vminvq_u8(x);
}
+static inline double simdHorizontalAddDbl(SimdDbl x) {
+ return vaddvq_f64(x);
+}
+
static inline SimdUint1 simdChoose1(SimdUint1 items, SimdUint1 choices) {
return vqtbl1q_u8(items, choices);
}
@@ -403,19 +507,29 @@ static inline SimdUint1 simdChoose1(SimdUint1 items, SimdUint1 choices) {
#else
typedef int SimdInt;
+typedef double SimdDbl;
const int simdBytes = 1;
const int simdLen = 1;
+const int simdDblLen = 1;
static inline int simdZero() { return 0; }
+static inline double simdZeroDbl() { return 0; }
static inline int simdSet(int x) { return x; }
+static inline double simdSetDbl(double x) { return x; }
static inline int simdFill(int x) { return x; }
static inline int simdLoad(const int *p) { return *p; }
+static inline double simdLoadDbl(const double *p) { return *p; }
static inline void simdStore(int *p, int x) { *p = x; }
+static inline void simdStoreDbl(double *p, double x) { *p = x; }
+static inline double simdFillDbl(double x) { return x; }
static inline int simdGt(int x, int y) { return x > y; }
static inline int simdAdd(int x, int y) { return x + y; }
+static inline double simdAddDbl(double x, double y) { return x + y; }
static inline int simdSub(int x, int y) { return x - y; }
+static inline double simdMulDbl(double x, double y) { return x * y; }
static inline int simdMax(int x, int y) { return x > y ? x : y; }
static inline int simdBlend(int x, int y, int mask) { return mask ? y : x; }
static inline int simdHorizontalMax(int a) { return a; }
+static inline double simdHorizontalAddDbl(double x) { return x; }
#endif
=====================================
src/split/last-split.cc
=====================================
@@ -27,23 +27,39 @@ static std::istream& openIn(const std::string& fileName, std::ifstream& ifs) {
}
// Does the string start with the prefix?
-static bool startsWith(const std::string& s, const char* prefix) {
- const char* t = s.c_str();
+static bool startsWith(const char *s, const char *prefix) {
for (;;) {
if (*prefix == 0) return true;
- if (*prefix != *t) return false;
- ++t;
+ if (*prefix != *s) return false;
+ ++s;
++prefix;
}
}
// Does the string have no non-space characters?
-static bool isSpace(const std::string& s) {
- const char* t = s.c_str();
+static bool isBlankLine(const char *s) {
for (;;) {
- if (*t == 0) return true;
- if (!std::isspace(*t)) return false;
- ++t;
+ if (*s == 0) return true;
+ if (!std::isspace(*s)) return false;
+ ++s;
+ }
+}
+
+static bool isSpace(char c) {
+ return c > 0 && c <= ' ';
+}
+
+static bool isSameName(const char *sLine1, const char *sLine2) {
+ do { ++sLine1; } while (isSpace(*sLine1));
+ do { ++sLine2; } while (isSpace(*sLine2));
+ for (;;) {
+ if (*sLine1 > ' ') {
+ if (*sLine2 != *sLine1) return false;
+ } else {
+ return *sLine2 <= ' ';
+ }
+ ++sLine1;
+ ++sLine2;
}
}
@@ -321,12 +337,15 @@ void lastSplit(LastSplitOptions& opts) {
double genomeSize = 0;
std::vector<std::string> mafLines; // lines of multiple MAF blocks
std::vector<unsigned> mafEnds(1); // which lines are in which MAF block
+ unsigned sLineCount = 0;
+ unsigned qNameLineNum = 0;
bool isAlreadySplit = false; // has the input already undergone last-split?
for (unsigned i = 0; i < opts.inputFileNames.size(); ++i) {
std::ifstream inFileStream;
std::istream& input = openIn(opts.inputFileNames[i], inFileStream);
while (getline(input, line)) {
+ const char *linePtr = line.c_str();
if (state == -1) { // we are reading the score matrix within the header
std::istringstream ls(line);
std::vector<int> row;
@@ -352,7 +371,7 @@ void lastSplit(LastSplitOptions& opts) {
if (word == "#" && !names.empty() && !ls && scoreMatrix.empty()) {
colNames = names;
state = -1;
- } else if (startsWith(line, "#")) {
+ } else if (linePtr[0] == '#') {
std::istringstream ls(line);
while (ls >> word) {
std::istringstream ws(word);
@@ -367,8 +386,8 @@ void lastSplit(LastSplitOptions& opts) {
if (key == "letters") ws >> genomeSize;
}
// try to determine if last-split was already run (fragile):
- if (startsWith(line, "# m=")) isAlreadySplit = true;
- } else if (!isSpace(line)) {
+ if (startsWith(linePtr, "# m=")) isAlreadySplit = true;
+ } else if (!isBlankLine(linePtr)) {
if (scoreMatrix.empty())
err("I need a header with score parameters");
if (gapExistenceCost < 0 || gapExtensionCost < 0 ||
@@ -410,18 +429,20 @@ void lastSplit(LastSplitOptions& opts) {
}
}
if (state == 1) { // we are reading alignments
- if (startsWith(line, "# batch") && !opts.isTopSeqQuery) {
+ if (isBlankLine(linePtr)) {
addMaf(mafEnds, mafLines);
- doOneBatch(mafLines, mafEnds, sa, opts, isAlreadySplit);
- mafLines.clear();
- mafEnds.resize(1);
- } else if (isSpace(line)) {
- addMaf(mafEnds, mafLines);
- } else if (std::strchr(opts.no_split ? "asqpc" : "sqpc", line[0])) {
+ } else if (std::strchr(opts.no_split ? "asqpc" : "sqpc", linePtr[0])) {
+ if (!opts.isTopSeqQuery && linePtr[0] == 's' && sLineCount++ % 2 &&
+ !isSameName(mafLines[qNameLineNum].c_str(), linePtr)) {
+ doOneBatch(mafLines, mafEnds, sa, opts, isAlreadySplit);
+ mafLines.erase(mafLines.begin(), mafLines.begin()+mafEnds.back());
+ mafEnds.resize(1);
+ qNameLineNum = mafLines.size();
+ }
mafLines.push_back(line);
}
}
- if (startsWith(line, "#") && !startsWith(line, "# batch"))
+ if (linePtr[0] == '#' && !startsWith(linePtr, "# batch"))
std::cout << line << "\n";
}
}
=====================================
src/tantan.cc
=====================================
@@ -1,6 +1,7 @@
// Copyright 2010 Martin C. Frith
#include "tantan.hh"
+#include "mcf_simd.hh"
#include <algorithm> // fill, max
#include <cassert>
@@ -14,6 +15,8 @@
namespace tantan {
+using namespace mcf;
+
void multiplyAll(std::vector<double> &v, double factor) {
for (std::vector<double>::iterator i = v.begin(); i < v.end(); ++i)
*i *= factor;
@@ -308,15 +311,37 @@ struct Tantan {
}
double b = backgroundProb;
- double fromForeground = 0;
- double *foregroundBeg = BEG(foregroundProbs);
+ const double *b2f = BEG(b2fProbs);
+ double *fp = BEG(foregroundProbs);
const double *lrRow = likelihoodRatioMatrix[*seqPtr];
int maxOffset = maxOffsetInTheSequence();
-
- for (int i = 0; i < maxOffset; ++i) {
- double f = foregroundBeg[i];
+ const uchar *sp = seqPtr;
+
+ SimdDbl bV = simdFillDbl(b);
+ SimdDbl tV = simdFillDbl(f2f0);
+ SimdDbl sV = simdZeroDbl();
+
+ int i = 0;
+ for (; i <= maxOffset - simdDblLen; i += simdDblLen) {
+ SimdDbl rV = simdSetDbl(
+#if defined __SSE4_1__ || defined __ARM_NEON
+#ifdef __AVX2__
+ lrRow[sp[-i-4]],
+ lrRow[sp[-i-3]],
+#endif
+ lrRow[sp[-i-2]],
+#endif
+ lrRow[sp[-i-1]]);
+ SimdDbl fV = simdLoadDbl(fp+i);
+ sV = simdAddDbl(sV, fV);
+ SimdDbl xV = simdMulDbl(bV, simdLoadDbl(b2f+i));
+ simdStoreDbl(fp+i, simdMulDbl(simdAddDbl(xV, simdMulDbl(fV, tV)), rV));
+ }
+ double fromForeground = simdHorizontalAddDbl(sV);
+ for (; i < maxOffset; ++i) {
+ double f = fp[i];
fromForeground += f;
- foregroundBeg[i] = (b * b2fProbs[i] + f * f2f0) * lrRow[seqPtr[-i-1]];
+ fp[i] = (b * b2f[i] + f * f2f0) * lrRow[sp[-i-1]];
}
backgroundProb = b * b2b + fromForeground * f2b;
@@ -330,15 +355,36 @@ struct Tantan {
}
double toBackground = f2b * backgroundProb;
- double toForeground = 0;
- double *foregroundBeg = BEG(foregroundProbs);
+ const double *b2f = BEG(b2fProbs);
+ double *fp = BEG(foregroundProbs);
const double *lrRow = likelihoodRatioMatrix[*seqPtr];
int maxOffset = maxOffsetInTheSequence();
-
- for (int i = 0; i < maxOffset; ++i) {
- double f = foregroundBeg[i] * lrRow[seqPtr[-i-1]];
- toForeground += b2fProbs[i] * f;
- foregroundBeg[i] = toBackground + f2f0 * f;
+ const uchar *sp = seqPtr;
+
+ SimdDbl bV = simdFillDbl(toBackground);
+ SimdDbl tV = simdFillDbl(f2f0);
+ SimdDbl sV = simdZeroDbl();
+
+ int i = 0;
+ for (; i <= maxOffset - simdDblLen; i += simdDblLen) {
+ SimdDbl rV = simdSetDbl(
+#if defined __SSE4_1__ || defined __ARM_NEON
+#ifdef __AVX2__
+ lrRow[sp[-i-4]],
+ lrRow[sp[-i-3]],
+#endif
+ lrRow[sp[-i-2]],
+#endif
+ lrRow[sp[-i-1]]);
+ SimdDbl fV = simdMulDbl(simdLoadDbl(fp+i), rV);
+ sV = simdAddDbl(sV, simdMulDbl(simdLoadDbl(b2f+i), fV));
+ simdStoreDbl(fp+i, simdAddDbl(bV, simdMulDbl(tV, fV)));
+ }
+ double toForeground = simdHorizontalAddDbl(sV);
+ for (; i < maxOffset; ++i) {
+ double f = fp[i] * lrRow[sp[-i-1]];
+ toForeground += b2f[i] * f;
+ fp[i] = toBackground + f2f0 * f;
}
backgroundProb = b2b * backgroundProb + toForeground;
=====================================
test/SRR359290-1k.maf
=====================================
The diff for this file was not included because it is too large.
=====================================
test/bs100.maf
=====================================
@@ -10,6 +10,54 @@ s 1 0 87 + 87 TTATATAGAGGAGATAAGTCGTAATATGGTAAGTGTATTGGAAAGTGTATTTGGATG
q 1 BB at 1;?@B at BBBC@BBBCACBBA>B??=?A at B?B?B=7 at 4BB;B>@@@A?>=B at A@>@7>BA>BA6BA?@@B@@?B?AABBAB=<>B
p $(-16:@FLRW]bddfgfccedffdedffdfgfdedeccfggggfdedecbcfgfdfgfddfggfdedfecba`]WTOKF@:40+'$
+a score=364 mismap=8.24e-08
+s chrM 12300 84 + 16571 GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAAT
+s 2 3 84 + 87 GGTTTTAAAAATTTTGGTGTAATTTTAAATAAAAGTAATAATTATGTATATTATTATAATTATTCTAACTTTGATTTTTTTAAT
+q 2 B at B>BB?B;=B@@=BBABA@<A5??'8@@>=3 at 47>@+AA9?;@@>@9?@(A>-9 at A=(=>?1;=7=96 at .4<(49=.2.1(==
+p &+.158>DJPUWZ]_dededfecbbbegfdfgggfdffdffccedededdbcdccedfeccdbbbbb_ZWTQNID@=:741.*$
+
+a score=258 mismap=8.71e-08
+s chrM 12453 69 + 16571 TGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTAT
+s 3 18 69 - 87 AATTGCATCCACCATTACTATCAATCTCTTCCCCCCAACAATATTCATATACCCAAACCAAAAAATGAT
+q 3 #52%7;3,5>BA4)9?+%+@<11>AA;*4:)383)CB=)+7*;8BB4>@@966)(BBAA<?@='?()>B
+p #%()-26<BGJOQQVZ[Z_adeccfggfggffd`Z^`acbbddfgfcc_\WTOIHHFEA<852/,)%%#
+
+a score=408 mismap=8.02e-08
+s chrM 5737 87 + 16571 CGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGA
+s 4 0 87 + 87 CGTCGTCGGGAAAAAAGGCGGGAGAAGTTTCGGTAGGTTTGAAGCTGTTTTTTCGAATTTGTAATTTAATATGAAAATTATTTCGGA
+q 4 ?BCC@?CCBCC at CBCACCCCCCCC@ABCCAABBCCBC at A=B at CBCACCC@BCB@?CCACBCBBBBB>C>@>BBB?BBB:=<B at B>BB
+p $),059<BHNTZ_dfggfdgggggggfcbbcffdfgfcccfggfccdbbaaabcfffcbcedffcbcffdecda\VPJFC>:741,&
+
+a score=280 mismap=9.01e-08
+s chrM 6086 87 + 16571 TGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCC
+s 5 0 87 - 87 TGGGTTCTTCTTAGCAACTGTTATAATAATACCCATCATAATCGAAAACTTTAACAACTAACAAATTCCCCTAATAATCGATACCCC
+q 5 ######################A8</<B::6>?@>@@?5>7/?B68@/B.A4BC<BB;B3B?BB>C5BB=>@>CBBABAABCCC?CB
+p !!!"""####$$$%%&''(*+-169=BEINRX]abefdeccfecbbbcfggfccdcbb_ZVSNQU[`dfggea_]XURMGC@;72,&
+
+a score=368 mismap=8.65e-08
+s chrM 11106 87 + 16571 TCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACG
+s 6 0 87 + 87 TTATATTTTATATTTTTTTCGAAATTATATTTATTTTTATTTTGGTTATTATTATTCGATGAGGTAATTAGTTAGAATGTCTGAACG
+q 6 BBB?C<@BA;5AB:AB at B?B<AB>A<AB:@AB9;=@AA43A>@;,5=@@A@/@>@=:?:@>><>-=6 at 746?=05?*?<<==9775=
+p $(-058;?BGKORTVWYZ\^begfccedecbcdbbbbbdbbbcefccecceccdcbcffdfggfdffccfecba]XRMID@=:50*&
+
+a score=340 mismap=9.13e-08
+s chrM 143 85 + 16571 CCTCATTCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAG
+s 7 2 85 - 87 CCTAATTCTCTTATCTATCGCTCCTACATTCAATATTACAAGCAAACATACCTACTAAAATATATTAATTAATTAATACTTATAA
+q 7 ####;672++4<=.060?>+/+22(9<;9;;94@@1=5=B:)?BA at BBBA98>4+:?<BB?@>:,6?B;BBCBCBBCBCC>@CCB
+p #%')-38;<=ADEFFKOTXYYW]accedfgfccedffdecbbdbbcededfgfdffcbbcededffcced`^\WQNJEB<71-($
+
+a score=368 mismap=8.66e-08
+s chrM 5006 87 + 16571 AGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTA
+s 8 0 87 + 87 AGTATATTCTTTAATTATTTATATAGGATGAATAATAGTAGTTTTATCGTATAATTTTAATATATCTATTTTTAATTTAATTATTTA
+q 8 B at C=BBCCBC?CCCC>BCC<B;@B@@BA2>C:<ABCC<A at A=@BB- at B?:B<B7>?AB:A@@@>(:AB@=B;B at BB>@<@>@A at ABB
+p &+/48=@CFILPUY\^`aabddedfggfdfgfdffdffdffcbbcdccededfecbbcefddb`\^`ba``^]ZVPMIFA<84/,(%
+
+a score=375 mismap=9.32e-08
+s chrM 7901 87 + 16571 TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGA
+s 9 0 87 + 87 TGAATTTACGAGTATATCGATTACGGTGGATTAATTTTTAATTTTTATATATTTTTTTTATTATTTTTAGAATTAGGTGATTTGCGA
+q 9 B=9=B+BBBB>BBB=:BB@;<@@B:<A4@?A:?=BABAAAA>>@<A>@AA>@@@?@@6878:6588?<:>=?9<::=<51<99>;48
+p $*058;?DHNTY\`bdccffccedffdfgfccfecbbbceecbbbcededebbaaaabbdccdbbbbcfggea_]YSMID>:74/+&
+
a score=207 mismap=1.15e-07
s chrM 3290 60 + 16571 ttcctcttcttaacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAA
s 10 0 60 + 87 TTTTTTTTTTTAATCATATATTTATGGTTAATTTTTTATTTTTTATTGTATTTATTCTAA
@@ -64,12 +112,6 @@ s 19 0 87 + 87 ACAATATATATTTTAATAAATAATGTTTAATTGGTAATTATTATTAATTAACGTTT
q 19 =@9 at B>C<';>)*8?'>67 at 1;(?<;A<@:@@(9A@@)(38>9+@<8?6 at 4:=?B976/5<@>@@/@<?1:0'9178--9=:426>@
p &*/58=AEGJKKNRW\_cffdfedecbcec_]Z_addbbdcceccffccffdecbcedffccededfggeb`_^\ZURMIFA;72,&
-a score=364 mismap=8.24e-08
-s chrM 12300 84 + 16571 GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAAT
-s 2 3 84 + 87 GGTTTTAAAAATTTTGGTGTAATTTTAAATAAAAGTAATAATTATGTATATTATTATAATTATTCTAACTTTGATTTTTTTAAT
-q 2 B at B>BB?B;=B@@=BBABA@<A5??'8@@>=3 at 47>@+AA9?;@@>@9?@(A>-9 at A=(=>?1;=7=96 at .4<(49=.2.1(==
-p &+.158>DJPUWZ]_dededfecbbbegfdfgggfdffdffccedededdbcdccedfeccdbbbbb_ZWTQNID@=:741.*$
-
a score=329 mismap=1.29e-07
s chrM 5859 87 + 16571 TTACAGTCCAATGCTTCACTCAGCCATTTTACCTCACCCCCACTGATGTTCGCCGACCGTTGACTATTCTCTACAAACCACAAAGAC
s 20 0 87 + 87 TTATAGTTTAATGTTTTATTTAGTTATTTTATTTTATTTTTACTGATGTTCGTCGATCGTTGATTATTATTTATAGATTATAAAGAT
@@ -130,12 +172,6 @@ s 29 0 81 + 87 AGTAATAAAATTAGGAATAGTTTTTTTTTATTTTTGAGTTTTAGAGGTTATTTAAGG
q 29 ?6 at C@5<(<CCB.CA?4BB=4?AA;=@CA=A<%=5>BB=15=B=>>6<B??):=>-<BA>(<@2;+%,?0805.'A7>(=;
p &+/5:>DIOTW[`dfgfdfecbaaaaabbdba`abeffcbbcfgggfccdbacfggfddb```_^\ZWROIFB?:62.+'$
-a score=258 mismap=8.71e-08
-s chrM 12453 69 + 16571 TGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTAT
-s 3 18 69 - 87 AATTGCATCCACCATTACTATCAATCTCTTCCCCCCAACAATATTCATATACCCAAACCAAAAAATGAT
-q 3 #52%7;3,5>BA4)9?+%+@<11>AA;*4:)383)CB=)+7*;8BB4>@@966)(BBAA<?@='?()>B
-p #%()-26<BGJOQQVZ[Z_adeccfggfggffd`Z^`acbbddfgfcc_\WTOIHHFEA<852/,)%%#
-
a score=349 mismap=1.08e-07
s chrM 6055 87 + 16571 ACCACATCTACAACGTTATCGTCACAGCCCATGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCA
s 30 0 87 + 87 ATTATATTTATAACGTTATCGTTATAGTTTATGTATTTGTAATAATTTTTTTTATAGTAATATTTATTAGAATCGGAGGTTTTGGTC
@@ -196,12 +232,6 @@ s 39 0 87 + 87 AATGGTATTGAATTTACGAGTATATCGATTACGGTGGATTAATTTTTAATTTTTATA
q 39 B?=BBBBB?B at BABBB=@BABBAAA at BBAA>;0===8>=;7.5:<;@@@A@<8A>351:@A2(;>@9-;73:7;<34.962+:=;.6
p &+/5:>CFJPVZ]_addfgfdedeccffccedffdfgfccfecbbbceecbbbcededebaa`aaabdba`\YVSPMHB=7321.)&
-a score=408 mismap=8.02e-08
-s chrM 5737 87 + 16571 CGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGA
-s 4 0 87 + 87 CGTCGTCGGGAAAAAAGGCGGGAGAAGTTTCGGTAGGTTTGAAGCTGTTTTTTCGAATTTGTAATTTAATATGAAAATTATTTCGGA
-q 4 ?BCC@?CCBCC at CBCACCCCCCCC@ABCCAABBCCBC at A=B at CBCACCC@BCB@?CCACBCBBBBB>C>@>BBB?BBB:=<B at B>BB
-p $),059<BHNTZ_dfggfdgggggggfcbbcffdfgfcccfggfccdbbaaabcfffcbcedffcbcffdecda\VPJFC>:741,&
-
a score=354 mismap=8.27e-08
s chrM 5186 87 + 16571 ACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGGAGGCCTGCCCCCGCTAACCGGCTTTTTGCCCAAATGGGCCATTATCGA
s 40 0 87 + 87 ATTAATATTTTTAATTTTATTTATTTTTTTTTTTTTAGGAGGTTTGTTTTCGTTAATCGGTTTTTTGTCTAAATGGGTTATTATTGA
@@ -262,12 +292,6 @@ s 49 0 87 + 87 TATGATTTATTTTATATTTTAATTTATGAGATTTATAATAAATAGTTTTTTTAAAT
q 49 BCBCBBCCCBB?BBB6CBCCB@@@BAA at C?BB at B@B@?BBC?B at B@@BBB>BBA5 at BB<>B=?@A4B>?>?BA==>?B?=@B:<=@B
p $*-38;>BGJMPTY\``abceecbcedfggfcbcedffdfgfdfecbaaabcfgfdeccfecccfffcba``\YVSPKGD?<83.($
-a score=280 mismap=9.01e-08
-s chrM 6086 87 + 16571 TGCATTTGTAATAATCTTCTTCATAGTAATACCCATCATAATCGGAGGCTTTGGCAACTGACTAGTTCCCCTAATAATCGGTGCCCC
-s 5 0 87 - 87 TGGGTTCTTCTTAGCAACTGTTATAATAATACCCATCATAATCGAAAACTTTAACAACTAACAAATTCCCCTAATAATCGATACCCC
-q 5 ######################A8</<B::6>?@>@@?5>7/?B68@/B.A4BC<BB;B3B?BB>C5BB=>@>CBBABAABCCC?CB
-p !!!"""####$$$%%&''(*+-169=BEINRX]abefdeccfecbbbcfggfccdcbb_ZVSNQU[`dfggea_]XURMGC@;72,&
-
a score=151 mismap=1.69e-07
s chrM 6025 36 + 16571 TGGGCCAGCCAGGCAACCTTCTAGGTAACGACCACA
s 50 0 36 + 87 TGGGTTAGTTAGGTAATTTTTTAGGTAACGATGATA
@@ -328,12 +352,6 @@ s 59 5 82 - 87 CTACGCCTAATACTAACATTCTATAAATATAATTTAGCTATTTCTATATATCTCCAT
q 59 ###?1@<AA>/@)+;6=3,=4)7:<9A@@>:@A>B?)420>99A5 at AB<?<>6=?B?BBAB:*0A?B-B9BA>B:>@8=ACB
p "#&+/5;@CGLPUY\^`^\WRVZ^_abdceccfgfcbefdfgggfdededfggggdfgfdfebcdbbaaaa^YSMID>82,&
-a score=368 mismap=8.65e-08
-s chrM 11106 87 + 16571 TCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACG
-s 6 0 87 + 87 TTATATTTTATATTTTTTTCGAAATTATATTTATTTTTATTTTGGTTATTATTATTCGATGAGGTAATTAGTTAGAATGTCTGAACG
-q 6 BBB?C<@BA;5AB:AB at B?B<AB>A<AB:@AB9;=@AA43A>@;,5=@@A@/@>@=:?:@>><>-=6 at 746?=05?*?<<==9775=
-p $(-058;?BGKORTVWYZ\^begfccedecbcdbbbbbdbbbcefccecceccdcbcffdfggfdffccfecba]XRMID@=:50*&
-
a score=383 mismap=8.82e-08
s chrM 12614 87 + 16571 CATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTAC
s 60 0 87 - 87 CATTATTCGTTACATAATCCATCATAAAATTCTCACTATAATATATAAACTCAAACCCAAACATTAATCAATTCTTCAAATCTCTAC
@@ -382,12 +400,6 @@ s 69 0 87 + 87 GATTAATGGGATTTAAATTTAAAAATATTTAGTTAATAGTTAAGTATTTTAATTAAT
q 69 B>BB;1ABB?@9ABAABAB at 4)?@A>(@>>*>>53A<>0@>@BAA@:7;)@<?AA at AB2',(@((0A@>?=7:>?A at B:@'?.<###
p &+/28=AGMSWZ]`dfeba`^Z_cecdbbcdeccffdffccfgfdecbbbeeccffccedbaaacda_][VROLIFC@=852-*'$"
-a score=340 mismap=9.13e-08
-s chrM 143 85 + 16571 CCTCATTCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAG
-s 7 2 85 - 87 CCTAATTCTCTTATCTATCGCTCCTACATTCAATATTACAAGCAAACATACCTACTAAAATATATTAATTAATTAATACTTATAA
-q 7 ####;672++4<=.060?>+/+22(9<;9;;94@@1=5=B:)?BA at BBBA98>4+:?<BB?@>:,6?B;BBCBCBBCBCC>@CCB
-p #%')-38;<=ADEFFKOTXYYW]accedfgfccedffdecbbdbbcededfgfdffcbbcededffcced`^\WQNJEB<71-($
-
a score=340 mismap=8.71e-08
s chrM 7675 84 + 16571 CATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGC
s 70 0 84 + 87 TATTTTTTTTATTTGTTTTTTAGTTTTGTATGTTTTTTTTTTAATATTTATAATAAAATTAATTAATATTAATATTTTAGACGT
@@ -448,12 +460,6 @@ s 79 0 87 + 87 ATTTGAATTAATATAATTATTTATAGTTTAATTATTAGTATTATTTTTTTATTATT
q 79 BCC?BCBBBACB?B:B>4B:9B>A<@@B at BBBA=B?9 at AB@AA9BA9?@@A14=BB@>B>@B8@@?@:4:0=<A>@<A>><85:;22
p %),06;@DHMRV[^bdccdcbcedffcbcefcceccffdeccdbbaaabbdccdbbaabcefccfgfcceeba\WSNHDA>952/*$
-a score=368 mismap=8.66e-08
-s chrM 5006 87 + 16571 AGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTA
-s 8 0 87 + 87 AGTATATTCTTTAATTATTTATATAGGATGAATAATAGTAGTTTTATCGTATAATTTTAATATATCTATTTTTAATTTAATTATTTA
-q 8 B at C=BBCCBC?CCCC>BCC<B;@B@@BA2>C:<ABCC<A at A=@BB- at B?:B<B7>?AB:A@@@>(:AB@=B;B at BB>@<@>@A at ABB
-p &+/48=@CFILPUY\^`aabddedfggfdfgfdffdffdffcbbcdccededfecbbcefddb`\^`ba``^]ZVPMIFA<84/,(%
-
a score=359 mismap=9.42e-08
s chrM 8356 87 + 16571 TTACAGTGAAATGCCCCAACTAAATACTACCGTATGGCCCACCATAATTACCCCCATACTCCTTACACTATTCCTCATCACCCAACT
s 81 0 87 + 87 TTATAGTGAAATGTTTTAATTAAATATTATCGTATGGTTTATTATAATTATTTTTATATTTTTTATATTATTTTTTATTATTTAATT
@@ -502,12 +508,6 @@ s 89 0 87 + 87 TTTTATATTTTTTATATTATTTTTTATTATTTAATTAAAAATATTAAATATAAATTA
q 89 9B:):<CCCAC>C:CCAC==B?CCCCCCCCB at BBCBCB<CBCCCB9?<B6BBA;B>CCC at C@<74C=CA/(;8@;-<3B at C=)%51C
p $'*-26:=@CGJNSV[]`bbaaabbdccdcbcefccfgggfdeccfgfdfdfgfcceccdcbcdbbaaa```a]ZXSMGA=:730,&
-a score=375 mismap=9.32e-08
-s chrM 7901 87 + 16571 TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGA
-s 9 0 87 + 87 TGAATTTACGAGTATATCGATTACGGTGGATTAATTTTTAATTTTTATATATTTTTTTTATTATTTTTAGAATTAGGTGATTTGCGA
-q 9 B=9=B+BBBB>BBB=:BB@;<@@B:<A4@?A:?=BABAAAA>>@<A>@AA>@@@?@@6878:6588?<:>=?9<::=<51<99>;48
-p $*058;?DHNTY\`bdccffccedffdfgfccfecbbbceecbbbcededebbaaaabbdccdbbbbcfggea_]YSMID>:74/+&
-
a score=278 mismap=1.03e-07
s chrM 1598 66 + 16571 CGAACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGAC
s 90 21 66 - 87 CTAACCAAAATATAACTTAACACAAAACACCCAACTTACACTTAAAAAATTTCAACTTAACTTAAC
=====================================
test/last-split-test.out
=====================================
@@ -4816,13 +4816,6 @@ s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
p &,28>DJPV\bhntz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-p "$&(*,.02468:<>@BDFHJLNPRTVX^djpv|~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -5027,6 +5020,12 @@ s SRR359290.9998 0 75 - 75 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGC
q SRR359290.9998 ECCE?DECDD==A=CDEBAECDE?FFG?EEFFGFFGEEDF=EEGGGGEGFGFGGGGGGGGGGGFGFGGFGAFGDG
p &,15788888888888888888888888888888888888888888888888888888888888888888751,&
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+p "$&(*,.02468:<>@BDFHJLNPRTVX^djpv|~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -8938,12 +8937,6 @@ s chr7 2702653 75 + 159138663 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGATGTTTGCTGTGCTTCCCGCCGTGGAGGGCAGAGCC
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -9099,6 +9092,11 @@ s chr15 79183831 75 + 102531392 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGC
s SRR359290.9998 0 75 - 75 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTCGGAAGAAAAGGGCCCGGGTAGATCCTACTG
q SRR359290.9998 ECCE?DECDD==A=CDEBAECDE?FFG?EEFFGFFGEEDF=EEGGGGEGFGFGGGGGGGGGGGFGFGGFGAFGDG
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -13059,12 +13057,6 @@ s chr7 2702653 75 + 159138663 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGATGTTTGCTGTGCTTCCCGCCGTGGAGGGCAGAGCC
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -13230,6 +13222,11 @@ s chr15 79183831 75 + 102531392 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGC
s SRR359290.9998 0 75 - 75 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTCGGAAGAAAAGGGCCCGGGTAGATCCTACTG
q SRR359290.9998 ECCE?DECDD==A=CDEBAECDE?FFG?EEFFGFFGEEDF=EEGGGGEGFGFGGGGGGGGGGGFGFGGFGAFGDG
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -17217,12 +17214,6 @@ s chr7 2702653 75 + 159138663 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGATGTTTGCTGTGCTTCCCGCCGTGGAGGGCAGAGCC
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -17388,6 +17379,11 @@ s chr15 79183831 75 + 102531392 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGC
s SRR359290.9998 0 75 - 75 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGCCTCCTCGGAAGAAAAGGGCCCGGGTAGATCCTACTG
q SRR359290.9998 ECCE?DECDD==A=CDEBAECDE?FFG?EEFFGFFGEEDF=EEGGGGEGFGFGGGGGGGGGGGFGFGGFGAFGDG
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -20918,12 +20914,6 @@ s chr7 2702653 75 + 159138663 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGATGTTTGCTGTGCTTCCCGCCGTGGAGGGCAGAGCC
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -21054,6 +21044,11 @@ s chrM 2277 75 + 16571 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC
s SRR359290.9997 0 75 + 75 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA
q SRR359290.9997 C55BCCCCCBC=CCBCB4CC8C@=CBBCCBBB=CC=CCCB=A?CBCCC4BC?BB?BCBBBABBBCC??BB?BBBB
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -25850,13 +25845,6 @@ s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
p &,28>DJPV\bhntz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-p "$&(*,.02468:<>@BDFHJLNPRTVX^djpv|~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -26061,6 +26049,12 @@ s SRR359290.9998 0 75 - 75 GAAATGGAGATGGTGGCAGTACCAGTGAGACCCCTCAGC
q SRR359290.9998 ECCE?DECDD==A=CDEBAECDE?FFG?EEFFGFFGEEDF=EEGGGGEGFGFGGGGGGGGGGGFGFGGFGAFGDG
p &,15788888888888888888888888888888888888888888888888888888888888888888751,&
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+p "$&(*,.02468:<>@BDFHJLNPRTVX^djpv|~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -30457,13 +30451,6 @@ s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -30632,6 +30619,12 @@ s SRR359290.9997 0 75 + 75 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC
q SRR359290.9997 C55BCCCCCBC=CCBCB4CC8C@=CBBCCBBB=CC=CCCB=A?CBCCC4BC?BB?BCBBBABBBCC??BB?BBBB
p }}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -35028,13 +35021,6 @@ s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -35203,6 +35189,12 @@ s SRR359290.9997 0 75 + 75 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC
q SRR359290.9997 C55BCCCCCBC=CCBCB4CC8C@=CBBCCBBB=CC=CCCB=A?CBCCC4BC?BB?BCBBBABBBCC??BB?BBBB
p }}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}
+a score=334 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -39599,13 +39591,6 @@ s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
q SRR359290.9962 AABA>=C?DBEEEEEEEEEEBEEEBAEBEE?EDEAEBDEDEEB?D=?B:@:ABA@@C@@A??B@@??BEB:??B2
p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-# CPU time: 2.52 seconds
-a score=334 mismap=1e-10 sense=0
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
-p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
a score=450 mismap=1e-10 sense=0
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -39774,6 +39759,12 @@ s SRR359290.9997 0 75 + 75 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC
q SRR359290.9997 C55BCCCCCBC=CCBCB4CC8C@=CBBCCBBB=CC=CCCB=A?CBCCC4BC?BB?BCBBBABBBCC??BB?BBBB
p }}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}}
+a score=334 mismap=1e-10 sense=0
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+q SRR359290.10000 ############################B13BB:B1;*6 at CCC=CACCC3A9A>12:;+9A;>2+A6AA=C?:5?
+p ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
# LAST version 356
#
# a=21 b=9 A=21 B=9 c=100000 F=-1 e=120 d=115 x=119 y=44 z=119
@@ -43479,12 +43470,6 @@ s chr7 2702653 75 + 159138663 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGA
s SRR359290.9962 0 75 + 75 AGCGAGGCTCCCCAATGGTGCTTTTGGCTTTAGTGTACGATGTTTGCTGTGCTTCCCGCCGTGGAGGGCAGAGCC
p &,28>DJPV\bhntz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-# CPU time: 2.52 seconds
-a score=426 mismap=1e-10
-s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
-p &,28>DJPV\bhntz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
-
a score=450 mismap=1e-10
s chr17 72765010 75 + 81195210 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
s SRR359290.9964 0 75 - 75 CCTCCTCCTCACTGAGTGCCTCATCCTACCGGGTGTCCCTTTGCCACCCTGCCTGGGACATCGCTGGAACCTGCA
@@ -43615,6 +43600,11 @@ s chrM 2277 75 + 16571 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAAC
s SRR359290.9997 0 75 + 75 CTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGA
p &,28>DJPV\bhnsxz{{|||||||||||||||||||||||||||||||||||||||{{zxsnhb\VPJD>82,&
+a score=426 mismap=1e-10
+s chr12 110785491 75 + 133851895 AATGTTTGCGCATGTTCGAGATGAGTCTCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+s SRR359290.10000 0 75 - 75 AATGTTTGCGCATGTTCGAGATGAGTCGCACCAACAGTGTGTAAGTCATTAACAGTCCTAACTGTGGTGTTTTCC
+p &,28>DJPV\bhntz~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ztnhb\VPJD>82,&
+
# LAST version 761
#
# a=14 b=3 A=19 B=3 e=110 d=90 x=109 y=44 z=109 D=10 E=1.70365e+07
=====================================
test/maf-convert-test.out
=====================================
The diff for this file was not included because it is too large.
=====================================
test/maf-swap-test.out
=====================================
@@ -20,6 +20,54 @@ q 1 BB at 1;?@B at BBBC@BBBCACBBA>B??=?A at B?B?B=7 at 4BB;B>@@@A?>=B at A@>
s chrM 1543 87 + 16571 TTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACACAAAGCACCC
p $(-16:@FLRW]bddfgfccedffdedffdfgfdedeccfggggfdedecbcfgfdfgfddfggfdedfecba`]WTOKF@:40+'$
+a score=364 mismap=8.24e-08
+s 2 3 84 + 87 GGTTTTAAAAATTTTGGTGTAATTTTAAATAAAAGTAATAATTATGTATATTATTATAATTATTCTAACTTTGATTTTTTTAAT
+q 2 B at B>BB?B;=B@@=BBABA@<A5??'8@@>=3 at 47>@+AA9?;@@>@9?@(A>-9 at A=(=>?1;=7=96 at .4<(49=.2.1(==
+s chrM 12300 84 + 16571 GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAAT
+p &+.158>DJPUWZ]_dededfecbbbegfdfgggfdffdffccedededdbcdccedfeccdbbbbb_ZWTQNID@=:741.*$
+
+a score=258 mismap=8.71e-08
+s 3 0 69 + 87 ATCATTTTTTGGTTTGGGTATATGAATATTGTTGGGGGGAAGAGATTGATAGTAATGGTGGATGCAATT
+q 3 B>)(?'=@?<AABB()669@@>4BB8;*7+)=BC)383):4*;AA>11<@+%+?9)4AB>5,3;7%25#
+s chrM 4049 69 - 16571 ATAACTTCTTGGTCTAGGCACATGAATATTGTTGTGGGGAAGAGACTGATAATAAAGGTGGATGCGACA
+p #%%),/258<AEFHHIOTW\_ccfgfddbbca`^Z`dffggfggfcceda_Z[ZVQQOJGB<62-)(%#
+
+a score=408 mismap=8.02e-08
+s 4 0 87 + 87 CGTCGTCGGGAAAAAAGGCGGGAGAAGTTTCGGTAGGTTTGAAGCTGTTTTTTCGAATTTGTAATTTAATATGAAAATTATTTCGGA
+q 4 ?BCC@?CCBCC at CBCACCCCCCCC@ABCCAABBCCBC at A=B at CBCACCC@BCB@?CCACBCBBBBB>C>@>BBB?BBB:=<B at B>BB
+s chrM 5737 87 + 16571 CGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGA
+p $),059<BHNTZ_dfggfdgggggggfcbbcffdfgfcccfggfccdbbaaabcfffcbcedffcbcffdecda\VPJFC>:741,&
+
+a score=280 mismap=9.01e-08
+s 5 0 87 + 87 GGGGTATCGATTATTAGGGGAATTTGTTAGTTGTTAAAGTTTTCGATTATGATGGGTATTATTATAACAGTTGCTAAGAAGAACCCA
+q 5 BC?CCCBAABABBC>@>=BB5C>BB?B3B;BB<CB4A.B/@86B?/7>5?@@>@?>6::B</<8A######################
+s chrM 10398 87 - 16571 GGGGCACCGATTATTAGGGGAACTAGTCAGTTGCCAAAGCCTCCGATTATGATGGGTATTACTATGAAGAAGATTATTACAAATGCA
+p &,27;@CGMRUX]_aeggfd`[UQNSVZ_bbcdccfggfcbbbcefccedfeba]XRNIEB=961-+*(''&%%$$$####"""!!!
+
+a score=368 mismap=8.65e-08
+s 6 0 87 + 87 TTATATTTTATATTTTTTTCGAAATTATATTTATTTTTATTTTGGTTATTATTATTCGATGAGGTAATTAGTTAGAATGTCTGAACG
+q 6 BBB?C<@BA;5AB:AB at B?B<AB>A<AB:@AB9;=@AA43A>@;,5=@@A@/@>@=:?:@>><>-=6 at 746?=05?*?<<==9775=
+s chrM 11106 87 + 16571 TCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACG
+p $(-058;?BGKORTVWYZ\^begfccedecbcdbbbbbdbbbcefccecceccdcbcffdfggfdffccfecba]XRMID@=:50*&
+
+a score=340 mismap=9.13e-08
+s 7 0 85 + 87 TTATAAGTATTAATTAATTAATATATTTTAGTAGGTATGTTTGCTTGTAATATTGAATGTAGGAGCGATAGATAAGAGAATTAGG
+q 7 BCC@>CCBCBBCBCBB;B?6,:>@?BB<?:+4>89ABBB at AB?):B=5=1@@49;;9;<9(22+/+>?060.=<4++276;####
+s chrM 16343 85 - 16571 CTACAAGCATTAATTAATTAACACACTTTAGTAGGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGAATGAGG
+p $(-17<BEJNQW\^`deccffdedecbbcffdfgfdedecbbdbbcedffdeccfgfdecca]WYYXTOKFFEDA=<;83-)'%#
+
+a score=368 mismap=8.66e-08
+s 8 0 87 + 87 AGTATATTCTTTAATTATTTATATAGGATGAATAATAGTAGTTTTATCGTATAATTTTAATATATCTATTTTTAATTTAATTATTTA
+q 8 B at C=BBCCBC?CCCC>BCC<B;@B@@BA2>C:<ABCC<A at A=@BB- at B?:B<B7>?AB:A@@@>(:AB@=B;B at BB>@<@>@A at ABB
+s chrM 5006 87 + 16571 AGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTA
+p &+/48=@CFILPUY\^`aabddedfggfdfgfdffdffdffcbbcdccededfecbbcefddb`\^`ba``^]ZVPMIFA<84/,(%
+
+a score=375 mismap=9.32e-08
+s 9 0 87 + 87 TGAATTTACGAGTATATCGATTACGGTGGATTAATTTTTAATTTTTATATATTTTTTTTATTATTTTTAGAATTAGGTGATTTGCGA
+q 9 B=9=B+BBBB>BBB=:BB@;<@@B:<A4@?A:?=BABAAAA>>@<A>@AA>@@@?@@6878:6588?<:>=?9<::=<51<99>;48
+s chrM 7901 87 + 16571 TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGA
+p $*058;?DHNTY\`bdccffccedffdfgfccfecbbbceecbbbcededebbaaaabbdccdbbbbcfggea_]YSMID>:74/+&
+
a score=207 mismap=1.15e-07
s 10 0 60 + 87 TTTTTTTTTTTAATCATATATTTATGGTTAATTTTTTATTTTTTATTGTATTTATTCTAA
q 10 @6)>B+A9<)?>>A(?A=-(48/<5?=1>4>:B@@<-:@@5;/9==ABA47*5':B<###
@@ -74,12 +122,6 @@ q 19 =@9 at B>C<';>)*8?'>67 at 1;(?<;A<@:@@(9A@@)(38>9+@<8?6 at 4:=?B9
s chrM 14174 87 + 16571 ACAATATATACACCAACAAACAATGTTCAACCAGTAACCACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGA
p &*/58=AEGJKKNRW\_cffdfedecbcec_]Z_addbbdcceccffccffdecbcedffccededfggeb`_^\ZURMIFA;72,&
-a score=364 mismap=8.24e-08
-s 2 3 84 + 87 GGTTTTAAAAATTTTGGTGTAATTTTAAATAAAAGTAATAATTATGTATATTATTATAATTATTCTAACTTTGATTTTTTTAAT
-q 2 B at B>BB?B;=B@@=BBABA@<A5??'8@@>=3 at 47>@+AA9?;@@>@9?@(A>-9 at A=(=>?1;=7=96 at .4<(49=.2.1(==
-s chrM 12300 84 + 16571 GGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAAT
-p &+.158>DJPUWZ]_dededfecbbbegfdfgggfdffdffccedededdbcdccedfeccdbbbbb_ZWTQNID@=:741.*$
-
a score=329 mismap=1.29e-07
s 20 0 87 + 87 TTATAGTTTAATGTTTTATTTAGTTATTTTATTTTATTTTTACTGATGTTCGTCGATCGTTGATTATTATTTATAGATTATAAAGAT
q 20 )@,27 at CBC:1?>C?-2AA?59'<)?B7A46)@>:*?8,5)<24?)5>?;?(2@@2(1>-:<3 at B5,<,3>7)?2%81,;@@BAA?B
@@ -140,12 +182,6 @@ q 29 ?6 at C@5<(<CCB.CA?4BB=4?AA;=@CA=A<%=5>BB=15=B=>>6<B??):=>-<
s chrM 4775 81 + 16571 AGCAATAAAACTAGGAATAGCCCCCTTTCACTTCTGAGTCCCAGAGGTTACCCAAGGCACCCCTCTGACATCCGGCCTGCT
p &+/5:>DIOTW[`dfgfdfecbaaaaabbdba`abeffcbbcfgggfccdbacfggfddb```_^\ZWROIFB?:62.+'$
-a score=258 mismap=8.71e-08
-s 3 0 69 + 87 ATCATTTTTTGGTTTGGGTATATGAATATTGTTGGGGGGAAGAGATTGATAGTAATGGTGGATGCAATT
-q 3 B>)(?'=@?<AABB()669@@>4BB8;*7+)=BC)383):4*;AA>11<@+%+?9)4AB>5,3;7%25#
-s chrM 4049 69 - 16571 ATAACTTCTTGGTCTAGGCACATGAATATTGTTGTGGGGAAGAGACTGATAATAAAGGTGGATGCGACA
-p #%%),/258<AEFHHIOTW\_ccfgfddbbca`^Z`dffggfggfcceda_Z[ZVQQOJGB<62-)(%#
-
a score=349 mismap=1.08e-07
s 30 0 87 + 87 ATTATATTTATAACGTTATCGTTATAGTTTATGTATTTGTAATAATTTTTTTTATAGTAATATTTATTAGAATCGGAGGTTTTGGTC
q 30 BB@<BBCBBBB at ABBB>ABB at B>BBA3>-@>BBCABAB>B6:+4BB;B8C?@?B=@BB?A;@?A?B@@B at BB@>-@:@?:>@A81>#
@@ -206,12 +242,6 @@ q 39 B?=BBBBB?B at BABBB=@BABBAAA at BBAA>;0===8>=;7.5:<;@@@A@<8A>35
s chrM 7893 87 + 16571 AATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCG
p &+/5:>CFJPVZ]_addfgfdedeccffccedffdfgfccfecbbbceecbbbcededebaa`aaabdba`\YVSPMHB=7321.)&
-a score=408 mismap=8.02e-08
-s 4 0 87 + 87 CGTCGTCGGGAAAAAAGGCGGGAGAAGTTTCGGTAGGTTTGAAGCTGTTTTTTCGAATTTGTAATTTAATATGAAAATTATTTCGGA
-q 4 ?BCC@?CCBCC at CBCACCCCCCCC@ABCCAABBCCBC at A=B at CBCACCC@BCB@?CCACBCBBBBB>C>@>BBB?BBB:=<B at B>BB
-s chrM 5737 87 + 16571 CGCCGCCGGGAAAAAAGGCGGGAGAAGCCCCGGCAGGTTTGAAGCTGCTTCTTCGAATTTGCAATTCAATATGAAAATCACCTCGGA
-p $),059<BHNTZ_dfggfdgggggggfcbbcffdfgfcccfggfccdbbaaabcfffcbcedffcbcffdecda\VPJFC>:741,&
-
a score=354 mismap=8.27e-08
s 40 0 87 + 87 ATTAATATTTTTAATTTTATTTATTTTTTTTTTTTTAGGAGGTTTGTTTTCGTTAATCGGTTTTTTGTCTAAATGGGTTATTATTGA
q 40 BB?BBBBBBBBCBBABBAB?B@@B<9BAB>BA at BBB<@BA at ABAAAB=:@BB:BAAB=<>@?4<@B at A@?9=?@=.4?9:+778;32
@@ -272,12 +302,6 @@ q 49 BCBCBBCCCBB?BBB6CBCCB@@@BAA at C?BB at B@B@?BBC?B at B@@BBB>BBA5@
s chrM 12896 87 + 16571 CATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCC
p $*-38;>BGJMPTY\``abceecbcedfggfcbcedffdfgfdfecbaaabcfgfdeccfecccfffcba``\YVSPKGD?<83.($
-a score=280 mismap=9.01e-08
-s 5 0 87 + 87 GGGGTATCGATTATTAGGGGAATTTGTTAGTTGTTAAAGTTTTCGATTATGATGGGTATTATTATAACAGTTGCTAAGAAGAACCCA
-q 5 BC?CCCBAABABBC>@>=BB5C>BB?B3B;BB<CB4A.B/@86B?/7>5?@@>@?>6::B</<8A######################
-s chrM 10398 87 - 16571 GGGGCACCGATTATTAGGGGAACTAGTCAGTTGCCAAAGCCTCCGATTATGATGGGTATTACTATGAAGAAGATTATTACAAATGCA
-p &,27;@CGMRUX]_aeggfd`[UQNSVZ_bbcdccfggfcbbbcefccedfeba]XRNIEB=961-+*(''&%%$$$####"""!!!
-
a score=151 mismap=1.69e-07
s 50 0 36 + 87 TGGGTTAGTTAGGTAATTTTTTAGGTAACGATGATA
q 50 ?)3<2A>:>*?6<B8>@7BB@<@B@>B0*(26)8B<
@@ -338,12 +362,6 @@ q 59 BCA=8@>:B>AB9B-B?A0*:BABB?B?=6><?<BA at 5A99>024)?B>A@:>@@A9
s chrM 6572 82 - 16571 AAAAGAGTAAGACCCTCATCAATAGATGGAGACATACAGAAATAGTCAAACCACATCTACAAAATGCCAGTATCAGGCGGCG
p &,28>DIMSY^aaaabbdcbefdfgfdggggfdededfgggfdfebcfgfccecdba_^ZVRW\^`^\YUPLGC@;5/+&#"
-a score=368 mismap=8.65e-08
-s 6 0 87 + 87 TTATATTTTATATTTTTTTCGAAATTATATTTATTTTTATTTTGGTTATTATTATTCGATGAGGTAATTAGTTAGAATGTCTGAACG
-q 6 BBB?C<@BA;5AB:AB at B?B<AB>A<AB:@AB9;=@AA43A>@;,5=@@A@/@>@=:?:@>><>-=6 at 746?=05?*?<<==9775=
-s chrM 11106 87 + 16571 TCATATTTTATATCTTCTTCGAAACCACACTTATCCCCACCTTGGCTATCATCACCCGATGAGGCAACCAGCCAGAACGCCTGAACG
-p $(-058;?BGKORTVWYZ\^begfccedecbcdbbbbbdbbbcefccecceccdcbcffdfggfdffccfecba]XRMID@=:50*&
-
a score=383 mismap=8.82e-08
s 60 0 87 + 87 GTAGAGATTTGAAGAATTGATTAATGTTTGGGTTTGAGTTTATATATTATAGTGAGAATTTTATGATGGATTATGTAACGAATAATG
q 60 B>B>=)=(@3:87/;7;(;:B8((:+@<)@7<B@:27(<ABAABAAB@=5()-@,1)>7.2A?@9=@?60((5=15A=31<@:?>@#
@@ -392,12 +410,6 @@ q 69 B>BB;1ABB?@9ABAABAB at 4)?@A>(@>>*>>53A<>0@>@BAA@:7;)@<?AA at A
s chrM 5660 87 + 16571 GACCAATGGGACTTAAACCCACAAACACTTAGTTAACAGCTAAGCACCCTAATCAACTGGCTTCAATCTACTTCTCCCGCCGCCGGG
p &+/28=AGMSWZ]`dfeba`^Z_cecdbbcdeccffdffccfgfdecbbbeeccffccedbaaacda_][VROLIFC@=852-*'$"
-a score=340 mismap=9.13e-08
-s 7 0 85 + 87 TTATAAGTATTAATTAATTAATATATTTTAGTAGGTATGTTTGCTTGTAATATTGAATGTAGGAGCGATAGATAAGAGAATTAGG
-q 7 BCC@>CCBCBBCBCBB;B?6,:>@?BB<?:+4>89ABBB at AB?):B=5=1@@49;;9;<9(22+/+>?060.=<4++276;####
-s chrM 16343 85 - 16571 CTACAAGCATTAATTAATTAACACACTTTAGTAGGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGAATGAGG
-p $(-17<BEJNQW\^`deccffdedecbbcffdfgfdedecbbdbbcedffdeccfgfdecca]WYYXTOKFFEDA=<;83-)'%#
-
a score=340 mismap=8.71e-08
s 70 0 84 + 87 TATTTTTTTTATTTGTTTTTTAGTTTTGTATGTTTTTTTTTTAATATTTATAATAAAATTAATTAATATTAATATTTTAGACGT
q 70 ?ACBCCCCCACBCBCCC=CCC>@7BCAACCBCBC?CBCCACCCC at ACC?AC at BA<C>CACC?@CBBBC67;@)=@>@A*=:B at 8
@@ -458,12 +470,6 @@ q 79 BCC?BCBBBACB?B:B>4B:9B>A<@@B at BBBA=B?9 at AB@AA9BA9?@@A14=BB
s chrM 10826 87 + 16571 ATTTGAATCAACACAACCACCCACAGCCTAATTATTAGCATCATCCCCCTACTATTTTTTAACCAAATCAACAACAACCTATTTAGC
p %),06;@DHMRV[^bdccdcbcedffcbcefcceccffdeccdbbaaabbdccdbbaabcefccfgfcceeba\WSNHDA>952/*$
-a score=368 mismap=8.66e-08
-s 8 0 87 + 87 AGTATATTCTTTAATTATTTATATAGGATGAATAATAGTAGTTTTATCGTATAATTTTAATATATCTATTTTTAATTTAATTATTTA
-q 8 B at C=BBCCBC?CCCC>BCC<B;@B@@BA2>C:<ABCC<A at A=@BB- at B?:B<B7>?AB:A@@@>(:AB@=B;B at BB>@<@>@A at ABB
-s chrM 5006 87 + 16571 AGCATACTCCTCAATTACCCACATAGGATGAATAATAGCAGTTCTACCGTACAACCCTAACATAACCATTCTTAATTTAACTATTTA
-p &+/48=@CFILPUY\^`aabddedfggfdfgfdffdffdffcbbcdccededfecbbcefddb`\^`ba``^]ZVPMIFA<84/,(%
-
a score=359 mismap=9.42e-08
s 81 0 87 + 87 TTATAGTGAAATGTTTTAATTAAATATTATCGTATGGTTTATTATAATTATTTTTATATTTTTTATATTATTTTTTATTATTTAATT
q 81 @C<?BCCBCCB at CB@;BB=4@@>BCAAB at .0;B@@?C at BBA3>AC>8/B=A=C at B<C226A1>8B at B;A<98AB>>)>A?<@@8@<5
@@ -512,12 +518,6 @@ q 89 9B:):<CCCAC>C:CCAC==B?CCCCCCCCB at BBCBCB<CBCCCB9?<B6BBA;B>C
s chrM 8407 87 + 16571 CCCCATACTCCTTACACTATTCCTCATCACCCAACTAAAAATATTAAACACAAACTACCACCTACCTCCCTCACCAAAGCCCATAAA
p $'*-26:=@CGJNSV[]`bbaaabbdccdcbcefccfgggfdeccfgfdfdfgfcceccdcbcdbbaaa```a]ZXSMGA=:730,&
-a score=375 mismap=9.32e-08
-s 9 0 87 + 87 TGAATTTACGAGTATATCGATTACGGTGGATTAATTTTTAATTTTTATATATTTTTTTTATTATTTTTAGAATTAGGTGATTTGCGA
-q 9 B=9=B+BBBB>BBB=:BB@;<@@B:<A4@?A:?=BABAAAA>>@<A>@AA>@@@?@@6878:6588?<:>=?9<::=<51<99>;48
-s chrM 7901 87 + 16571 TGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGA
-p $*058;?DHNTY\`bdccffccedffdfgfccfecbbbceecbbbcededebbaaaabbdccdbbbbcfggea_]YSMID>:74/+&
-
a score=278 mismap=1.03e-07
s 90 0 66 + 87 GTTAAGTTAAGTTGAAATTTTTTAAGTGTAAGTTGGGTGTTTTGTGTTAAGTTATATTTTGGTTAG
q 90 8;'6=ABA;1BA.789AA9A>'))4BA??7)?=:(?<1)3 at AA>6<@:'.B@?-?:=328124:##
=====================================
test/maf-swap-test.sh
=====================================
@@ -16,4 +16,4 @@ PATH=../bin:$PATH
try maf-swap -n1 90089.maf
try maf-swap -n3 ../examples/multiMito.maf
try maf-swap frameshift-new.maf
-} 2>&1 | diff -u $(basename $0 .sh).out -
+} 2>&1 | diff -u maf-swap-test.out -
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/d66071ad838061ef3de19947217335b96bf2e96e...04dde6a254a5dacbed8eb4dc37426e605fecc37a
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/d66071ad838061ef3de19947217335b96bf2e96e...04dde6a254a5dacbed8eb4dc37426e605fecc37a
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