[med-svn] [Git][med-team/last-align][master] 5 commits: Add myself back to uploaders
Nilesh Patra (@nilesh)
gitlab at salsa.debian.org
Sat Dec 31 11:58:46 GMT 2022
Nilesh Patra pushed to branch master at Debian Med / last-align
Commits:
fc3168a7 by Nilesh Patra at 2022-12-31T17:16:13+05:30
Add myself back to uploaders
- - - - -
b38e2fed by Nilesh Patra at 2022-12-31T17:18:15+05:30
New upstream version 1420
- - - - -
c6f0c617 by Nilesh Patra at 2022-12-31T17:18:19+05:30
Update upstream source from tag 'upstream/1420'
Update to upstream version '1420'
with Debian dir 9d79de9dd248ebd0a9c9a3309322d08ce2007661
- - - - -
d4486409 by Nilesh Patra at 2022-12-31T17:18:22+05:30
Bump Standards-Version to 4.6.2 (no changes needed)
- - - - -
dd2ce64c by Nilesh Patra at 2022-12-31T17:18:33+05:30
Upload to unstable
- - - - -
9 changed files:
- bin/maf-convert
- debian/changelog
- debian/control
- doc/maf-convert.rst
- src/makefile
- test/frameshift-new.maf
- test/maf-convert-test.out
- test/maf-convert-test.sh
- test/maf-swap-test.out
Changes:
=====================================
bin/maf-convert
=====================================
@@ -360,6 +360,59 @@ def mafConvertToChain(opts, lines):
for maf in mafInput(opts, lines):
writeChain(maf)
+##### Routines for converting to BED format: #####
+
+def bedBlocksFromMafs(mafs, ref):
+ for i, x in enumerate(mafs):
+ beg, end = x[1][ref][4:6]
+ if not i:
+ origin = beg
+ yield end - beg, beg - origin
+
+def writeBed(opts, mafs):
+ headLines = mafs[0][1]
+ tailLines = mafs[-1][1]
+
+ if opts.subject:
+ ref = opts.subject - 1
+ elif len(headLines) > 1 and headLines[0][3] < headLines[1][3]:
+ ref = 1 # protein-to-DNA alignment
+ else:
+ ref = 0
+
+ if len(headLines) <= ref:
+ raise RuntimeError("alignment has too few sequences")
+
+ qry = 0 if ref > 0 else 1
+ qryName = headLines[qry][0] if len(headLines) > qry else "."
+ qryStrand = headLines[qry][2] if len(headLines) > qry else "+"
+
+ seqName, seqLen, strand, junk, beg = headLines[ref][:5]
+ end = tailLines[ref][5]
+ blocks = list(bedBlocksFromMafs(mafs, ref))
+
+ if strand == "-":
+ beg, end = seqLen - end, seqLen - beg
+ origin = sum(blocks[-1])
+ blocks = [(s, origin - b - s) for s, b in reversed(blocks)]
+
+ outStrand = "+" if qryStrand == strand else "-"
+ blockLens = ",".join(str(i[0]) for i in blocks)
+ blockBegs = ",".join(str(i[1]) for i in blocks)
+ print(seqName, beg, end, qryName, 0, outStrand, beg, beg, 0,
+ len(blocks), blockLens, blockBegs, sep="\t")
+
+def mafConvertToBed(opts, lines):
+ if opts.Join:
+ for i in colinearMafInput(opts, lines):
+ writeBed(opts, i)
+ elif opts.join:
+ for i in mafGroupInput(opts, lines):
+ writeBed(opts, i)
+ else:
+ for i in mafInput(opts, lines):
+ writeBed(opts, [i])
+
##### Routines for converting to PSL format: #####
def pslBlocks(opts, geneticCode, mafs, outCounts):
@@ -474,7 +527,8 @@ def writePsl(opts, geneticCode, mafs):
fieldsA, fieldsB = mafs[0][1]
- if fieldsA[3] < fieldsB[3]: # protein-to-DNA alignment
+ if opts.subject == 2 or fieldsA[3] < fieldsB[3] and opts.subject != 1:
+ # default for protein-to-DNA alignment
fieldsA, fieldsB = fieldsB, fieldsA
blocks = [(s, b, a) for s, a, b in blocks]
@@ -497,11 +551,13 @@ def writePsl(opts, geneticCode, mafs):
numInsertA, numInsertB = pslNumInserts(blocks, sizeMulA, sizeMulB)
- strand = strandB
if sizeMulA > 1 or sizeMulB > 1:
- strand += strandA
- elif strandA != "+":
- raise Exception("for non-translated PSL, the 1st strand in each alignment must be +")
+ strand = strandB + strandA
+ else:
+ strand = "+" if strandA == strandB else "-"
+ if strandA == "-":
+ blocks = [(s, seqLenA - a - s, seqLenB - b - s)
+ for s, a, b in reversed(blocks)]
blockCount = len(blocks)
blockSizes, blockStartsA, blockStartsB = map(pslCommaString, zip(*blocks))
@@ -721,7 +777,7 @@ def codonMatchSymbols(opts, geneticCode, aaSeq, ntSeq):
j = i + 3
a = aminoAcidCodes.get(aaSeq[i:j], "X")
b = ntSeq[i:j]
- if geneticCode.get(b, "X") == a:
+ if geneticCode.get(b, "Z") == a:
yield "|||"
else:
score = opts.scoreMatrix.get((a, b), -1)
@@ -801,6 +857,8 @@ def blastLineData(letterSize, beg, line):
def writeBlast(opts, geneticCode, codon2triplet, maf, oldQueryName):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "Blast")
+ if opts.subject == 2:
+ fieldsA, fieldsB = fieldsB, fieldsA
dataA = blastDataFromMafFields(fieldsA)
dataB = blastDataFromMafFields(fieldsB)
seqNameA, seqLenA, strandA, letterSizeA, begA, maxPosA, rowA, upA = dataA
@@ -879,11 +937,13 @@ def mafConvertToBlast(opts, lines):
aa2triplet = dict((j, i.title()) for i, j in aminoAcidCodes.items())
codon2triplet = dict((i, aa2triplet[j]) for i, j in geneticCode.items())
+ qryNum = 0 if opts.subject == 2 else 1
+
oldQueryName = ""
for maf in mafInput(opts, lines):
writeBlast(opts, geneticCode, codon2triplet, maf, oldQueryName)
sLines = maf[1]
- oldQueryName = sLines[1][0]
+ oldQueryName = sLines[qryNum][0]
def btabDataFromMafFields(fields):
seqName, seqLen, strand, letterSize, beg, end, row = fields
@@ -929,6 +989,8 @@ def codonMatchCounts(geneticCode, letterSizeA, letterSizeB, rowA, rowB):
def writeBlastTab(opts, geneticCode, maf):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "BlastTab")
+ if opts.subject == 2:
+ fieldsA, fieldsB = fieldsB, fieldsA
seqNameA, letterSizeA, begA, endA, rowA = btabDataFromMafFields(fieldsA)
seqNameB, letterSizeB, begB, endB, rowB = btabDataFromMafFields(fieldsB)
gapOpens = gapRunCount(rowA) + gapRunCount(rowB)
@@ -968,11 +1030,12 @@ def mafConvertToBlastTab(opts, lines):
def writeGffHeader():
print("##gff-version 3")
-def gffFromMaf(maf):
+def gffFromMaf(opts, maf):
aLine, sLines, qLines, pLines = maf
fieldsA, fieldsB = pairOrDie(sLines, "GFF")
- if fieldsA[3] < fieldsB[3]: # protein-to-DNA alignment
+ if opts.subject == 2 or fieldsA[3] < fieldsB[3] and opts.subject != 1:
+ # default for protein-to-DNA alignment
fieldsA, fieldsB = fieldsB, fieldsA
seqNameA, seqLenA, strandA, letterSizeA, begA, endA, rowA = fieldsA
@@ -1004,8 +1067,8 @@ def writeOneGff(gff, typeOfThing, parentId):
print(seqNameA, "maf-convert", typeOfThing, begA, endA, score, strand, ".",
";".join(attributes), sep="\t")
-def writeGffGroup(qryNameCounts, mafs):
- gffs = [gffFromMaf(i) for i in mafs]
+def writeGffGroup(opts, qryNameCounts, mafs):
+ gffs = sorted(gffFromMaf(opts, i) for i in mafs)
seqNameA, begA, endA, strand, score, seqNameB, begB, endB = gffs[0]
endA = gffs[-1][2]
if strand == "+":
@@ -1026,13 +1089,13 @@ def mafConvertToGff(opts, lines):
qryNameCounts = collections.defaultdict(int)
if opts.Join:
for i in colinearMafInput(opts, lines):
- writeGffGroup(qryNameCounts, i)
+ writeGffGroup(opts, qryNameCounts, i)
elif opts.join:
for i in mafGroupInput(opts, lines):
- writeGffGroup(qryNameCounts, i)
+ writeGffGroup(opts, qryNameCounts, i)
else:
for i in mafInput(opts, lines):
- writeOneGff(gffFromMaf(i), "match", None)
+ writeOneGff(gffFromMaf(opts, i), "match", None)
##### Routines for converting to HTML format: #####
@@ -1145,6 +1208,8 @@ def isFormat(myString, myFormat):
def mafConvertOneFile(opts, formatName, lines):
if isFormat(formatName, "axt"):
mafConvertToAxt(opts, lines)
+ elif isFormat(formatName, "bed"):
+ mafConvertToBed(opts, lines)
elif isFormat(formatName, "blast"):
mafConvertToBlast(opts, lines)
elif isFormat(formatName, "blasttab"):
@@ -1202,6 +1267,7 @@ if __name__ == "__main__":
usage = """
%prog --help
%prog axt mafFile(s)
+ %prog bed mafFile(s)
%prog blast mafFile(s)
%prog blasttab mafFile(s)
%prog chain mafFile(s)
@@ -1214,6 +1280,8 @@ if __name__ == "__main__":
description = "Read MAF-format alignments & write them in another format."
op = optparse.OptionParser(usage=usage, description=description)
+ op.add_option("-s", "--subject", type="int", metavar="N",
+ help="which sequence to use as subject/reference")
op.add_option("-p", "--protein", action="store_true",
help="assume protein alignments, for psl match counts")
op.add_option("-j", "--join", type="float", metavar="N", help="join "
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+last-align (1420-1) unstable; urgency=medium
+
+ * Add myself back to uploaders
+ * New upstream version 1420
+ * Bump Standards-Version to 4.6.2 (no changes needed)
+
+ -- Nilesh Patra <nilesh at debian.org> Sat, 31 Dec 2022 17:18:26 +0530
+
last-align (1418-1) unstable; urgency=medium
* New upstream version
=====================================
debian/control
=====================================
@@ -2,6 +2,7 @@ Source: last-align
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Charles Plessy <plessy at debian.org>,
Andreas Tille <tille at debian.org>,
+ Nilesh Patra <nilesh at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13),
@@ -10,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
zlib1g-dev,
libsimde-dev,
debhelper
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/last-align
Vcs-Git: https://salsa.debian.org/med-team/last-align.git
Homepage: https://gitlab.com/mcfrith/last
=====================================
doc/maf-convert.rst
=====================================
@@ -2,7 +2,7 @@ maf-convert
===========
This script reads alignments in maf_ format, and writes them in
-another format. It can write them in these formats: axt_, blast,
+another format. It can write them in these formats: axt_, bed_, blast,
blasttab, chain_, gff, html, psl_, sam, tab. You can use it like this::
maf-convert psl my-alignments.maf > my-alignments.psl
@@ -12,8 +12,8 @@ It's often convenient to pipe in the input, like this::
... | maf-convert psl > my-alignments.psl
This script takes the first (topmost) maf sequence as the "reference"
-/ "subject" / "target", and the second sequence as the "query".
-(Exception: when converting DNA-to-protein alignments to gff or psl,
+/ "subject", and the second sequence as the "query".
+(Exception: when converting DNA-to-protein alignments to bed, gff or psl,
the protein becomes the "query" and the DNA becomes the "reference".)
For html: if the input includes probability lines starting with 'p',
@@ -22,6 +22,7 @@ starting with 'p', run lastal with option -j set to 4 or higher.)
.. _maf: http://genome.ucsc.edu/FAQ/FAQformat.html#format5
.. _axt: https://genome.ucsc.edu/goldenPath/help/axt.html
+.. _bed: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
.. _chain: https://genome.ucsc.edu/goldenPath/help/chain.html
.. _psl: https://genome.ucsc.edu/FAQ/FAQformat.html#format2
@@ -31,6 +32,11 @@ Options
-h, --help
Print a help message and exit.
+-s N, --subject=N
+ Use the Nth sequence in each alignment as the "reference" /
+ "subject". This option affects these formats: bed, blast,
+ blasttab, gff, psl.
+
-p, --protein
Specify that the alignments are of proteins, rather than
nucleotides. This affects psl format only (the first 4
@@ -41,12 +47,12 @@ Options
the same sequences and strands, with the parts being in the
same order in each sequence), are separated by at most N
letters in each sequence, and are consecutive in the input.
- This affects psl and gff formats only.
+ This affects bed, gff, and psl formats only.
-J N, --Join=N
Join alignments that are co-linear, are separated by at most
N letters in each sequence, and are nearest in each sequence.
- This affects psl and gff formats only, and reads the whole
+ This affects bed, gff and psl formats only, and reads the whole
input into memory.
-n, --noheader
=====================================
src/makefile
=====================================
@@ -144,7 +144,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1418) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1420) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
test/frameshift-new.maf
=====================================
@@ -37,7 +37,7 @@
#
# batch 0
a score=3177.2 EG2=0 E=0
-s UN-L1MA6_pol#LINE/L1 657 616 + 1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly
+s UN-L1MA6_pol#LINE/L1 657 616 + 1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysXaa-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly
s chrUn_KI270748v1 13904 1811 + 93321 CAAGGGTGCCCACTCTCAGAACTTCTATTCAACATAGTACTGGATGTCCTAGCCAGAGCAATTAGGCAAAAGAAAGaaaTAAAAGGCATGAAAATTGGAAAGGAAGAAGTTAAATTGTTTCTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAATTCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAGGTGAATGATCTTTACACTGAAAACTACAAAACATTGATGAAAACAATTGAAGAAGCCACAAATAAATGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAATGTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAATTCCTATGACATTTTCCCACAGAAATAGAAAAACAACTCTCAAATCTGTATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCGAAAAAAGCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCTATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCAATTACACAGAATAAAGAGCCCATAAATAAATCTACAT---ATTATAGTCAATTGACTTTCAACAAAGGTGCCAGGAACACA---CATGGGGAAAGAACAGTCTCTTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGATCTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTT---AGACTTAAATGTAAGACCTAGCACTATAGAACTCCTAGAAGAAAAC---AGGGGAATAACTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGACTCTAAAGCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATCAACCTAAAAAGCTTCTGCGCAGCAAAAGAA---AGTCAACAGAGTGAAGTGATAACCTACAAAATGGGAGGAATTATCTGCAAACTATACATTTGATAAGAGGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAataataagaaAACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAGATATATA---AAAATGCTAATTATCACTGATCATCAGAGAAATGCATATTAAAACTACAATAAAATGCCATTTCACATCCGTTAGAATGGCTGTTACAGAAAAGGCAGAAGATACCAAGTGTTGGAGAGGATGTGGAGAAAAGGAAAACCTTGTA------ATTGTTGAGAATGTAAACTATTTCAGCCATTGTAAAAGACAGTATAAGTGATTCTG---------TAAAAATAGAATTACCATATGATTCAGTAATGCTATTTCTGGGCATATATTAAAAAGATATCAAATCAGTGTGTCAATGAGTTATCTGTACTCCCATATTTATTGTAGCATTATTCACAACAGCCAAGATGTGGAATTAACTTAAGTATCCATCGACACATGAGTGGATGAAGAAAATGTGGTACACATACACAATAGAATAGTATACAACCTTAaaaaataaaaaa---aGTATCATTTGTGACAACATGAATGAACCGGGAGGACATTATACTGAGTAAAATAATCCAGGCACAGAAAGCCAGATACTGCATAATCTCACTTGTATGTGGA
a score=1775.7 EG2=2.9e-164 E=1.5e-169
=====================================
test/maf-convert-test.out
=====================================
@@ -1,6 +1,7 @@
Usage:
maf-convert --help
maf-convert axt mafFile(s)
+ maf-convert bed mafFile(s)
maf-convert blast mafFile(s)
maf-convert blasttab mafFile(s)
maf-convert chain mafFile(s)
@@ -14,6 +15,7 @@ Read MAF-format alignments & write them in another format.
Options:
-h, --help show this help message and exit
+ -s N, --subject=N which sequence to use as subject/reference
-p, --protein assume protein alignments, for psl match counts
-j N, --join=N join consecutive co-linear alignments separated by <=
N letters
@@ -7393,7 +7395,7 @@ Sbjct: 658 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgG
LeuPheAlaValAspMetIleLeuTyrIleGluAsnThrAsnAsnSerAlaLysLys LeuGluPheIleAsnGluPheSerLysValAlaGlyTyrAsnValAsnIleGlnAsn
Query: 14025 CTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAAT 14139
||||||||| |||||||||||||||||||||||| ::::::|||:::|||||| ||||||:::||||||||||||||||||||||||||||||::::::|||||||||:::
-Sbjct: 698 LeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLys 736
+Sbjct: 698 LeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysXaa-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLys 736
SerValAlaPheLeuHisIleAsnAsnLysLeu ThrLysLysGluIleLysLysThrIleLeuPheIleIleAlaThrLys TyrLeuAspValAsnLeuAsnLysGlu
Query: 14140 TCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAG 14250
@@ -7843,6 +7845,191 @@ Query: 852 LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys 864
Sbjct: 18550 AAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa 18588
LysArgSerLeuIleAlaLysAlaLeuLeuSerLysLys
+Query= UN-L1MA6_pol#LINE/L1
+ (1275 letters)
+
+>chrUn_KI270748v1
+ Length = 93321
+
+ Score = 1559.7, Expect = 2e-147
+ Identities = 180/292 (61%), Gaps = 23/292 (7%)
+ Strand = Plus / Minus
+
+Query: 884 LysThrAlaTrpTyrTrpHisLys--AsnArgHisIleAspGlnTrpAsnArgIleGlu 902
+ |||||| |||||||||||||||||||||||||||||||||
+Sbjct: 90089 TaatcagcctggtaatcaCGT---AAAACAGACACATAGACCAGTGGAACAGAATAGAG 90034
+ ***SerAlaTrp***SerArg AsnArgHisIleAspGlnTrpAsnArgIleGlu
+
+Query: 903 SerProGluIleAsnProArgIleTyrSerGlnLeuIlePheAspLysGlyAlaLysAsn 922
+ ||| ||||||||| ||||||||||||||||||||| |||||| |||
+Sbjct: 90033 AACCCAGATATAAATCCACACATTTACAGCCAGCTCATCTTCAGCAAAGGCACCAACAAC 89974
+ AsnProAspIleAsnProHisIleTyrSerGlnLeuIlePheSerLysGlyThrAsnAsn
+
+Query: 923 ThrGlnTrp-GlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSer 941
+ |||||| |||||| ||||||||| ||| |||
+Sbjct: 89973 ATACGA---GCGAAAGGACGGTCTCTTCCATAAGTGGTGCAGGGGAAACTAGATAAAG 89919
+ IleArg ArgLysAspGlyLeuPheHisLysTrpCysArgGlyAsn***IleLys
+
+Query: 942 ThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLys 961
+ |||||||||||||||||||||||| ||| ||||||||| ||| |||
+Sbjct: 89918 ATATGCAGAAGAATGAAACTAGACCCGTCTCTCTTACCATACACAGAAATCAAATCAGAA 89859
+ IleCysArgArgMetLysLeuAspProSerLeuLeuProTyrThrGluIleLysSerGlu
+
+Query: 962 TrpIleLysAspLeu-AsnValArgProGluThrMetLysLeuLeuGluGluAsnIle 980
+ ||||||||| ||||||||| |||||||||||||||||||||
+Sbjct: 89858 TGGATTAAAGGT---AAAACTGAGACCTGAAAGTATAAAACTACTGGAAGAAAACATT 89804
+ TrpIleLysGly LysLeuArgProGluSerIleLysLeuLeuGluGluAsnIle
+
+Query: 981 GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAla 1000
+ ||| ||| |||||| ||| ||||||||| ||||||
+Sbjct: 89803 AGGGAAGTGCTCCAGGACATTGTTCTCAGCAAAGACTTTTTCAGTAGGGCCCCAAAAGCA 89744
+ ArgGluValLeuGlnAspIleValLeuSerLysAspPhePheSerArgAlaProLysAla
+
+Query: 1001 GlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThr 1020
+ |||||||||||||||||| |||||| |||||| |||
+Sbjct: 89743 CAGGCAACCAAAGCAAAAACAGACAAGTGAAATCACACCAAGCTAAGAACCCTCTGCAGA 89684
+ GlnAlaThrLysAlaLysThrAspLys***AsnHisThrLysLeuArgThrLeuCysArg
+
+Query: 1021 AlaLysGluThrIleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAla 1040
+ |||||| ||| |||||||||||||||||||||||||||||| |||
+Sbjct: 89683 CCAAAGGAAAAAGTCAACAAACTGAAGAGACAACCCACAGAATGGGAGAAAATACTTGCA 89624
+ ProLysGluLysValAsnLysLeuLysArgGlnProThrGluTrpGluLysIleLeuAla
+
+Query: 1041 AsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLys--GluLeuLysGlnLeu 1059
+ ||| ||||||||| ||| ||||||||||||
+Sbjct: 89623 AGCTACCCACCTGACAAGGGATTCATAACC------------AGGAGCTCAAACAA--- 89580
+ SerTyrProProAspLysGlyPheIleThr GluLeuLysGln
+
+Query: 1060 AsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPhe 1079
+ ||| ||| ||| ||||||||| |||||| |||||||||
+Sbjct: 89579 ------TAGCAAACAATTAATCGAATTTTAAAATGGGCAAGAGACCTGAGTAGACATTTC 89526
+ ***GlnThrIleAsnArgIleLeuLysTrpAlaArgAspLeuSerArgHisPhe
+
+Query: 1080 SerLysGluAspIleGlnMetAlaAsnArgTyrMetLysLysCysSerThrSerLeuIle 1099
+ |||||||||||| ||||||||| |||||||||||||||||||||||||||||||||
+Sbjct: 89525 TCAAAAGAAGATGTACAAATGGCCAGCAGGTACATGAAAAAATGCTCAACATCACTAATC 89466
+ SerLysGluAspValGlnMetAlaSerArgTyrMetLysLysCysSerThrSerLeuIle
+
+Query: 1100 IleArgGluMetGlnIle-LysThrThrMetArgTyrHisLeuThrProValArgMet 1118
+ ||||||||| |||||| |||||| |||||| |||||| ||| |||
+Sbjct: 89465 ATCAGAGAAACGCAAATAAAAAACTGCAATGAGGTCTTCTCTCACCTCAGTTAAAATG 89408
+ IleArgGluThrGlnIle LysThrAlaMetArgSerSerLeuThrSerValLysMet
+
+Query: 1119 AlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThr 1138
+ ||| ||| ||||||||||||||||||||| ||||||
+Sbjct: 89407 GCTTTCGTCAAAAACGCAGGGAATAAGGGATGCTGGCGAGGATGTGGAGAAAGGGGGACC 89348
+ AlaPheValLysAsnAlaGlyAsnLysGlyCysTrpArgGlyCysGlyGluArgGlyThr
+
+Query: 1139 LeuThrHisCysTrp--TrpGluCysLysLeuValGlnProLeuTrpLysThrVal-- 1156
+ |||||||||||| |||||| ||||||||||||||||||||||||
+Sbjct: 89347 CTCACACACTGT---TGTGGGAACGTTGATTAGTACAACCACTATGGAAAACA---GA 89296
+ LeuThrHisCys TrpGluArg***LeuValGlnProLeuTrpLysThr
+
+Query: 1157 TrpArgPheLeuLysLysLeuLys 1164
+ |||||| ||||||||| |||
+Sbjct: 89295 TGGAGGCTCCTCAaaaaaccaaaa 89272
+ TrpArgLeuLeuLysLysProLys
+
+Query= UN-L1PA16_pol#LINE/L1
+ (1276 letters)
+
+>chrUn_KI270748v1
+ Length = 93321
+
+ Score = 1508.0, Expect = 3.8e-142
+ Identities = 230/359 (64%), Gaps = 33/359 (9%)
+ Strand = Plus / Plus
+
+Query: 527 LysGluAsnTyrArgProIleSerLeuMetAsnIleAspAlaLysIleLeuAsnLysIle 546
+ |||||||||||| |||||| ||| ||| ||||||||||||||||||
+Sbjct: 17572 AAAGAAAACTACAAATCCTTATCCCTGATCAACACAGATGTAAAAATACTCAACAAAATT 17631
+ LysGluAsnTyrLysSerLeuSerLeuIleAsnThrAspValLysIleLeuAsnLysIle
+
+Query: 547 LeuAlaAsnArgIleGlnGlnHisIleLysLysLeuIleHisHisAspGlnValGlyPhe 566
+ ||||||||| ||||||||||||||| ||||||||||||||||||||||||
+Sbjct: 17632 CTAGCAAACTGAAGCTAACAACACATCAAAAAGATAATTCATCATGATCAAGTGGGCTTT 17691
+ LeuAlaAsn***Ser***GlnHisIleLysLysIleIleHisHisAspGlnValGlyPhe
+
+Query: 567 IleProGlyMetGlnGlyTrpPheAsnIleArgLysSerIleAsnValIleHisHisIle 586
+ ||||||||| |||||| ||| |||||||||||| ||||||||||||
+Sbjct: 17692 ATTCCAGGGGTGCTTGAATGGTTCAAAATAGACAAATCAATAAACATGATTCACCACATA 17751
+ IleProGlyValLeuGluTrpPheLysIleAspLysSerIleAsnMetIleHisHisIle
+
+Query: 587 AsnArgIleLysAsnLysAsnHisMetIleIleSerIleAspAlaGluLysAlaPheAsp 606
+ ||| ||||||||| |||||||||||| ||||||||| |||||||||
+Sbjct: 17752 AATGGAACTGAGAACAAAAACCCTATGATCATCTCATTAGATGCAGAATaagcatttgat 17811
+ AsnGlyThrGluAsnLysAsnProMetIleIleSerLeuAspAlaGlu***AlaPheAsp
+
+Query: 607 LysIleGlnHisProPheMetIleLysThrLeuXaaLysLeuGlyIleGluGlyThrTyr 626
+ |||||||||||| |||||||||||||||||| |||||| ||| |||
+Sbjct: 17812 aaaatccaacatctgtttatgataaaaaccctcaACAATATAGGTATAGATGGAGTATAC 17871
+ LysIleGlnHisLeuPheMetIleLysThrLeuAsnAsnIleGlyIleAspGlyValTyr
+
+Query: 627 LeuLysIleIleArgAlaIleTyrAspLysProThrAlaAsnIleIleLeuAsnGlyGln 646
+ |||||| |||||||||||| |||||||||||||||||| ||||||
+Sbjct: 17872 CTCAAA---AAATGAGTCATCTATGACAAAGCCACAGCCAACATCATCCTGGATGGGCAA 17928
+ LeuLys Lys***ValIleTyrAspLysAlaThrAlaAsnIleIleLeuAspGlyGln
+
+Query: 647 LysLeuGluAlaPheProLeuArgThrGlyThrArgGlnGlyCysProLeuSerProLeu 666
+ ||||||||| ||| |||||| ||||||||| |||
+Sbjct: 17929 AAGTTAGAAGTGTTGCTTCTAGAAACTGGAAAAAAGCAAGGATGTTCACCTTCATCATTC 17988
+ LysLeuGluValLeuLeuLeuGluThrGlyLysLysGlnGlyCysSerProSerSerPhe
+
+Query: 667 LeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLys 686
+ ||||||||| ||||||||||||||||||||| |||||| |||||||||||||||
+Sbjct: 17989 CTATTCAATACAGTACTGGAAGTGCTAGCCAGAACTATCAGAAAGGAGAAAGAAATAAAA 18048
+ LeuPheAsnThrValLeuGluValLeuAlaArgThrIleArgLysGluLysGluIleLys
+
+Query: 687 GlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeu 706
+ |||||||||||| ||| ||||||||| |||||| |||||||||
+Sbjct: 18049 GGTATACAAATTAGAAAA---GAAGTCAAATGATCTCTGCTCACTGATGACATGACTGTA 18105
+ GlyIleGlnIleArgLys GluValLys***SerLeuLeuThrAspAspMetThrVal
+
+Query: 707 TyrLeuGluAsnProLysAspSerAlaLysArgLeuLeuGluLeuIleAsnAspPheSer 726
+ ||||||||||||||| ||||||||| |||||| |||||||||
+Sbjct: 18106 GGCCTAGAAAACCCTAAAGTCTTC---AGAAGACTCCTAGACTTGATACACGACTTCAGT 18162
+ GlyLeuGluAsnProLysValPhe ArgArgLeuLeuAspLeuIleHisAspPheSer
+
+Query: 727 LysValSerGlyTyrLysIleAsnVal--GlnLysSerValAlaPheLeuTyrThrAsn 745
+ |||||| ||| |||||||||||| ||||||||||||
+Sbjct: 18163 AAAGTCTTGGGATAAACAAGC------CACAAAAATCAGTTGTATTTCTATACACCAAA 18215
+ LysValLeuGly***ThrSer GlnLysSerValValPheLeuTyrThrLys
+
+Query: 746 AsnValGlnAla-----------------------------GluSerGlnIleLysAsn 755
+ |||||| ||| ||||||||||||
+Sbjct: 18216 TACATTCAAGCTGTTTGAATGTTTGTTGAGATTAATTtgttgAGAACCAAATTAAGAAC 18274
+ TyrIleGlnAla GluAsnGlnIleLysAsn
+
+Query: 756 AlaIleProPheThrIleAlaThrLysLysIle--LysTyrLeuGlyIleHisLeu-Thr 774
+ |||||||||||| |||||||||||| ||| |||
+Sbjct: 18275 TCAACTGAATTTACAATAGCCATG---------AAAAATACCTAGGAATGCAT---AACT 18322
+ SerThrGluPheThrIleAlaMet LysTyrLeuGlyMetHis Thr
+
+Query: 775 LysGluValLysAspLeuTyrLysGluAsnTyrLysThrLeuLeuLysGluIleIleAsp 794
+ ||||||||||||||||||||||||||| ||| |||||||||||||||
+Sbjct: 18323 ATATAAATGAAAGATCTCTACAAGGAGAACTACAAAATACTAATGAAAGAAATTATAGAT 18382
+ Ile***MetLysAspLeuTyrLysGluAsnTyrLysIleLeuMetLysGluIleIleAsp
+
+Query: 795 AspThrAsnLysTrpLysAsnIleProCysSerTrpIleGlyArgIleAsnIle-Val 813
+ ||| ||||||||||||||||||||||||||||||||| ||||||
+Sbjct: 18383 GACATAAACAAATGGAAAAACATCCCATGCTCATGGATTAGAAAAATCAAT---AGCT 18437
+ AspIleAsnLysTrpLysAsnIleProCysSerTrpIleArgLysIleAsn Ala
+
+Query: 814 LysMetAlaIleLeuProLys--AlaIleTyrArgPheAsnAlaIleProIleLysLeu 832
+ ||| ||| ||| ||||||||| |||||||||||||||||||||
+Sbjct: 18438 AAAGTGACCATATCACCC---ATACAATCTATAGAGTTAATGCAATTCCCATCAAATTA 18493
+ LysValThrIleSerPro ThrIleTyrArgValAsnAlaIleProIleLysLeu
+
+Query: 833 ProMetSerPhePheThrGluLeuGluLysThr-IleLeuLysPheIleTrpAsnGln- 851
+ ||| ||| ||| ||| ||| |||||||||||| ||| |||
+Sbjct: 18494 CCAACGTTATTTCTCACAaaattaaaaaaa---aaTCCTAAAGTTCACATGGAGCCAAA 18549
+ ProThrLeuPheLeuThrLysLeuLysLys IleLeuLysPheThrTrpSerGln
+
+Query: 852 LysArgAlaGlnIleAlaLysAlaIleLeuSerLysLys 864
+ |||||| |||||||||||| ||||||||||||
+Sbjct: 18550 AAAAGATCCCTAATAGCCAAAGCACTTCTAAGCAAAAAa 18588
+ LysArgSerLeuIleAlaLysAlaLeuLeuSerLysLys
+
0 chrM 93.10 87 6 0 87 1 13914 14000
1 chrM 85.06 87 13 0 1 87 1544 1630
2 chrM 71.43 84 24 0 4 87 12301 12384
@@ -7943,6 +8130,11 @@ chrUn_KI270748v1 UN-L1PA2_pol#LINE/L1 93.39 227 15 0 3860 4540 1049 1275 1.5e-16
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 62.18 386 107 14 3661 2577 518 879 2.5e-152 546
chrUn_KI270748v1 UN-L1MA6_pol#LINE/L1 61.64 292 89 8 90089 89272 884 1164 2e-147 530
chrUn_KI270748v1 UN-L1PA16_pol#LINE/L1 64.07 359 96 11 17572 18588 527 864 3.8e-142 512
+UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 63.82 633 194 13 658 1273 13905 15715 0 1.08e+03
+UN-L1PA2_pol#LINE/L1 chrUn_KI270748v1 93.39 227 15 0 1049 1275 3860 4540 1.5e-169 603
+UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 62.18 386 107 14 518 879 3661 2577 2.5e-152 546
+UN-L1MA6_pol#LINE/L1 chrUn_KI270748v1 61.64 292 89 8 884 1164 90089 89272 2e-147 530
+UN-L1PA16_pol#LINE/L1 chrUn_KI270748v1 64.07 359 96 11 527 864 17572 18588 3.8e-142 512
chain 221 chr1 249250621 + 160106735 160106810 SRR359290.9001 75 - 0 75 1
75
chain 450 chr1 249250621 + 231468663 231468738 SRR359290.9002 75 + 0 75 2
@@ -8573,11 +8765,232 @@ chr19 maf-convert match_part 1395388 1395484 291 - . Target=102 4 102;Name=102:4
chr22 maf-convert match 20726589 20726617 . - . ID=102.73;Name=102:69-95
chr22 maf-convert match_part 20726589 20726617 115 - . Target=102 69 95;Name=102:69-95;Parent=102.73
##gff-version 3
+102 maf-convert match 7 28 . + . ID=chr5.1;Name=chr5:93489543-93489564
+102 maf-convert match_part 7 28 118 + . Target=chr5 93489543 93489564;Name=chr5:93489543-93489564;Parent=chr5.1
+102 maf-convert match 11 29 . + . ID=chr5.2;Name=chr5:74376578-74376596
+102 maf-convert match_part 11 29 114 + . Target=chr5 74376578 74376596;Name=chr5:74376578-74376596;Parent=chr5.2
+102 maf-convert match 88 112 . + . ID=chr3.1;Name=chr3:152862894-152862920
+102 maf-convert match_part 88 112 116 + . Target=chr3 152862894 152862920;Name=chr3:152862894-152862920;Parent=chr3.1
+102 maf-convert match 92 118 . + . ID=chr2.1;Name=chr2:240456632-240456656
+102 maf-convert match_part 92 118 125 + . Target=chr2 240456632 240456656;Name=chr2:240456632-240456656;Parent=chr2.1
+102 maf-convert match 141 159 . + . ID=chr1.1;Name=chr1:145870018-145870036
+102 maf-convert match_part 141 159 114 + . Target=chr1 145870018 145870036;Name=chr1:145870018-145870036;Parent=chr1.1
+102 maf-convert match 257 277 . + . ID=chr18.1;Name=chr18:55335093-55335113
+102 maf-convert match_part 257 277 112 + . Target=chr18 55335093 55335113;Name=chr18:55335093-55335113;Parent=chr18.1
+102 maf-convert match 372 403 . + . ID=chr19.1;Name=chr19:47072202-47072237
+102 maf-convert match_part 372 403 110 + . Target=chr19 47072202 47072237;Name=chr19:47072202-47072237;Parent=chr19.1
+102 maf-convert match 426 465 . + . ID=chr8.1;Name=chr8:76840859-76840909
+102 maf-convert match_part 426 465 117 + . Target=chr8 76840859 76840909;Name=chr8:76840859-76840909;Parent=chr8.1
+102 maf-convert match 434 454 . + . ID=chr4.1;Name=chr4:3839063-3839083
+102 maf-convert match_part 434 454 112 + . Target=chr4 3839063 3839083;Name=chr4:3839063-3839083;Parent=chr4.1
+102 maf-convert match 443 463 . + . ID=chr20.1;Name=chr20:4034148-4034168
+102 maf-convert match_part 443 463 110 + . Target=chr20 4034148 4034168;Name=chr20:4034148-4034168;Parent=chr20.1
+102 maf-convert match 443 463 . + . ID=chr3.2;Name=chr3:186865652-186865672
+102 maf-convert match_part 443 463 110 + . Target=chr3 186865652 186865672;Name=chr3:186865652-186865672;Parent=chr3.2
+102 maf-convert match 443 463 . + . ID=chr7.1;Name=chr7:65260307-65260327
+102 maf-convert match_part 443 463 110 + . Target=chr7 65260307 65260327;Name=chr7:65260307-65260327;Parent=chr7.1
+102 maf-convert match 459 490 . + . ID=chr1.2;Name=chr1:161050906-161050943
+102 maf-convert match_part 459 490 119 + . Target=chr1 161050906 161050943;Name=chr1:161050906-161050943;Parent=chr1.2
+102 maf-convert match 460 490 . + . ID=chr18.2;Name=chr18:8561209-8561245
+102 maf-convert match_part 460 490 114 + . Target=chr18 8561209 8561245;Name=chr18:8561209-8561245;Parent=chr18.2
+102 maf-convert match 465 494 . + . ID=chr17.1;Name=chr17:28925930-28925955
+102 maf-convert match_part 465 494 111 + . Target=chr17 28925930 28925955;Name=chr17:28925930-28925955;Parent=chr17.1
+102 maf-convert match 468 504 . + . ID=chr1.3;Name=chr1:21590631-21590682
+102 maf-convert match_part 468 504 121 + . Target=chr1 21590631 21590682;Name=chr1:21590631-21590682;Parent=chr1.3
+102 maf-convert match 468 491 . + . ID=chr15.1;Name=chr15:45614750-45614773
+102 maf-convert match_part 468 491 118 + . Target=chr15 45614750 45614773;Name=chr15:45614750-45614773;Parent=chr15.1
+102 maf-convert match 471 489 . + . ID=chr13.1;Name=chr13:113342216-113342234
+102 maf-convert match_part 471 489 114 + . Target=chr13 113342216 113342234;Name=chr13:113342216-113342234;Parent=chr13.1
+102 maf-convert match 471 489 . + . ID=chr17.2;Name=chr17:19079610-19079628
+102 maf-convert match_part 471 489 114 + . Target=chr17 19079610 19079628;Name=chr17:19079610-19079628;Parent=chr17.2
+102 maf-convert match 471 489 . + . ID=chr17.3;Name=chr17:19205792-19205810
+102 maf-convert match_part 471 489 114 + . Target=chr17 19205792 19205810;Name=chr17:19205792-19205810;Parent=chr17.3
+102 maf-convert match 471 489 . + . ID=chr22.1;Name=chr22:23657491-23657509
+102 maf-convert match_part 471 489 114 + . Target=chr22 23657491 23657509;Name=chr22:23657491-23657509;Parent=chr22.1
+102 maf-convert match 473 499 . + . ID=chr10.1;Name=chr10:122813035-122813060
+102 maf-convert match_part 473 499 120 + . Target=chr10 122813035 122813060;Name=chr10:122813035-122813060;Parent=chr10.1
+102 maf-convert match 473 491 . + . ID=chr5.3;Name=chr5:4867426-4867444
+102 maf-convert match_part 473 491 114 + . Target=chr5 4867426 4867444;Name=chr5:4867426-4867444;Parent=chr5.3
+102 maf-convert match 477 499 . + . ID=chr11.1;Name=chr11:67464147-67464169
+102 maf-convert match_part 477 499 124 + . Target=chr11 67464147 67464169;Name=chr11:67464147-67464169;Parent=chr11.1
+102 maf-convert match 480 508 . + . ID=chr14.1;Name=chr14:104715673-104715703
+102 maf-convert match_part 480 508 126 + . Target=chr14 104715673 104715703;Name=chr14:104715673-104715703;Parent=chr14.1
+102 maf-convert match 486 508 . + . ID=chr3.3;Name=chr3:127741376-127741402
+102 maf-convert match_part 486 508 112 + . Target=chr3 127741376 127741402;Name=chr3:127741376-127741402;Parent=chr3.3
+102 maf-convert match 488 512 . + . ID=chr5.4;Name=chr5:169763616-169763644
+102 maf-convert match_part 488 512 110 + . Target=chr5 169763616 169763644;Name=chr5:169763616-169763644;Parent=chr5.4
+102 maf-convert match 494 515 . + . ID=chr7.2;Name=chr7:157969524-157969545
+102 maf-convert match_part 494 515 114 + . Target=chr7 157969524 157969545;Name=chr7:157969524-157969545;Parent=chr7.2
+102 maf-convert match 509 533 . + . ID=chr5.5;Name=chr5:173701200-173701222
+102 maf-convert match_part 509 533 113 + . Target=chr5 173701200 173701222;Name=chr5:173701200-173701222;Parent=chr5.5
+102 maf-convert match 547 565 . + . ID=chr17.4;Name=chr17:27793640-27793658
+102 maf-convert match_part 547 565 114 + . Target=chr17 27793640 27793658;Name=chr17:27793640-27793658;Parent=chr17.4
+102 maf-convert match 619 638 . + . ID=chr10.2;Name=chr10:124281395-124281414
+102 maf-convert match_part 619 638 120 + . Target=chr10 124281395 124281414;Name=chr10:124281395-124281414;Parent=chr10.2
+102 maf-convert match 641 667 . + . ID=chr14.2;Name=chr14:80332130-80332156
+102 maf-convert match_part 641 667 118 + . Target=chr14 80332130 80332156;Name=chr14:80332130-80332156;Parent=chr14.2
+102 maf-convert match 667 693 . + . ID=chr21.1;Name=chr21:14291181-14291209
+102 maf-convert match_part 667 693 114 + . Target=chr21 14291181 14291209;Name=chr21:14291181-14291209;Parent=chr21.1
+102 maf-convert match 674 696 . + . ID=chr3.4;Name=chr3:23607557-23607579
+102 maf-convert match_part 674 696 138 + . Target=chr3 23607557 23607579;Name=chr3:23607557-23607579;Parent=chr3.4
+102 maf-convert match 681 699 . + . ID=chrX.1;Name=chrX:83302602-83302620
+102 maf-convert match_part 681 699 114 + . Target=chrX 83302602 83302620;Name=chrX:83302602-83302620;Parent=chrX.1
+102 maf-convert match 636 657 . - . ID=chr22.2;Name=chr22:46458801-46458822
+102 maf-convert match_part 636 657 115 - . Target=chr22 46458801 46458822;Name=chr22:46458801-46458822;Parent=chr22.2
+102 maf-convert match 626 646 . - . ID=chr19.2;Name=chr19:17615431-17615451
+102 maf-convert match_part 626 646 126 - . Target=chr19 17615431 17615451;Name=chr19:17615431-17615451;Parent=chr19.2
+102 maf-convert match 614 645 . - . ID=chr19.3;Name=chr19:1383911-1383942
+102 maf-convert match_part 614 645 178 - . Target=chr19 1383911 1383942;Name=chr19:1383911-1383942;Parent=chr19.3
+102 maf-convert match 605 637 . - . ID=chr10.3;Name=chr10:126932870-126932910
+102 maf-convert match_part 605 637 115 - . Target=chr10 126932870 126932910;Name=chr10:126932870-126932910;Parent=chr10.3
+102 maf-convert match 575 616 . - . ID=chr19.4;Name=chr19:1387808-1387847
+102 maf-convert match_part 575 616 215 - . Target=chr19 1387808 1387847;Name=chr19:1387808-1387847;Parent=chr19.4
+102 maf-convert match 507 575 . - . ID=chr19.5;Name=chr19:1388524-1388593
+102 maf-convert match_part 507 575 321 - . Target=chr19 1388524 1388593;Name=chr19:1388524-1388593;Parent=chr19.5
+102 maf-convert match 541 563 . - . ID=chr5.6;Name=chr5:177958542-177958564
+102 maf-convert match_part 541 563 111 - . Target=chr5 177958542 177958564;Name=chr5:177958542-177958564;Parent=chr5.6
+102 maf-convert match 510 533 . - . ID=chr15.2;Name=chr15:78230486-78230510
+102 maf-convert match_part 510 533 110 - . Target=chr15 78230486 78230510;Name=chr15:78230486-78230510;Parent=chr15.2
+102 maf-convert match 501 526 . - . ID=chr2.2;Name=chr2:192414463-192414489
+102 maf-convert match_part 501 526 115 - . Target=chr2 192414463 192414489;Name=chr2:192414463-192414489;Parent=chr2.2
+102 maf-convert match 503 526 . - . ID=chr3.5;Name=chr3:33026625-33026648
+102 maf-convert match_part 503 526 112 - . Target=chr3 33026625 33026648;Name=chr3:33026625-33026648;Parent=chr3.5
+102 maf-convert match 486 524 . - . ID=chr1.4;Name=chr1:155997874-155997913
+102 maf-convert match_part 486 524 110 - . Target=chr1 155997874 155997913;Name=chr1:155997874-155997913;Parent=chr1.4
+102 maf-convert match 484 524 . - . ID=chr7.3;Name=chr7:101590380-101590420
+102 maf-convert match_part 484 524 133 - . Target=chr7 101590380 101590420;Name=chr7:101590380-101590420;Parent=chr7.3
+102 maf-convert match 503 521 . - . ID=chr3.6;Name=chr3:89815480-89815498
+102 maf-convert match_part 503 521 114 - . Target=chr3 89815480 89815498;Name=chr3:89815480-89815498;Parent=chr3.6
+102 maf-convert match 486 510 . - . ID=chr3.7;Name=chr3:130609409-130609434
+102 maf-convert match_part 486 510 119 - . Target=chr3 130609409 130609434;Name=chr3:130609409-130609434;Parent=chr3.7
+102 maf-convert match 402 509 . - . ID=chr19.6;Name=chr19:1388830-1388938
+102 maf-convert match_part 402 509 495 - . Target=chr19 1388830 1388938;Name=chr19:1388830-1388938;Parent=chr19.6
+102 maf-convert match 485 509 . - . ID=chr8.2;Name=chr8:98433262-98433291
+102 maf-convert match_part 485 509 121 - . Target=chr8 98433262 98433291;Name=chr8:98433262-98433291;Parent=chr8.2
+102 maf-convert match 485 508 . - . ID=chr6.1;Name=chr6:170257702-170257727
+102 maf-convert match_part 485 508 110 - . Target=chr6 170257702 170257727;Name=chr6:170257702-170257727;Parent=chr6.1
+102 maf-convert match 489 507 . - . ID=chr12.1;Name=chr12:19357536-19357554
+102 maf-convert match_part 489 507 114 - . Target=chr12 19357536 19357554;Name=chr12:19357536-19357554;Parent=chr12.1
+102 maf-convert match 481 505 . - . ID=chr19.7;Name=chr19:18430560-18430588
+102 maf-convert match_part 481 505 124 - . Target=chr19 18430560 18430588;Name=chr19:18430560-18430588;Parent=chr19.7
+102 maf-convert match 485 503 . - . ID=chr21.2;Name=chr21:43027935-43027953
+102 maf-convert match_part 485 503 114 - . Target=chr21 43027935 43027953;Name=chr21:43027935-43027953;Parent=chr21.2
+102 maf-convert match 478 496 . - . ID=chr17.5;Name=chr17:29190070-29190088
+102 maf-convert match_part 478 496 114 - . Target=chr17 29190070 29190088;Name=chr17:29190070-29190088;Parent=chr17.5
+102 maf-convert match 458 491 . - . ID=chr7.4;Name=chr7:101723246-101723286
+102 maf-convert match_part 458 491 115 - . Target=chr7 101723246 101723286;Name=chr7:101723246-101723286;Parent=chr7.4
+102 maf-convert match 459 490 . - . ID=chr12.2;Name=chr12:71544987-71545025
+102 maf-convert match_part 459 490 129 - . Target=chr12 71544987 71545025;Name=chr12:71544987-71545025;Parent=chr12.2
+102 maf-convert match 471 489 . - . ID=chr17.6;Name=chr17:19172451-19172469
+102 maf-convert match_part 471 489 114 - . Target=chr17 19172451 19172469;Name=chr17:19172451-19172469;Parent=chr17.6
+102 maf-convert match 471 489 . - . ID=chr17.7;Name=chr17:58670491-58670509
+102 maf-convert match_part 471 489 114 - . Target=chr17 58670491 58670509;Name=chr17:58670491-58670509;Parent=chr17.7
+102 maf-convert match 471 489 . - . ID=chr6.2;Name=chr6:1842832-1842850
+102 maf-convert match_part 471 489 114 - . Target=chr6 1842832 1842850;Name=chr6:1842832-1842850;Parent=chr6.2
+102 maf-convert match 471 489 . - . ID=chr7.5;Name=chr7:100370597-100370615
+102 maf-convert match_part 471 489 114 - . Target=chr7 100370597 100370615;Name=chr7:100370597-100370615;Parent=chr7.5
+102 maf-convert match 471 489 . - . ID=chrX.2;Name=chrX:39928417-39928435
+102 maf-convert match_part 471 489 114 - . Target=chrX 39928417 39928435;Name=chrX:39928417-39928435;Parent=chrX.2
+102 maf-convert match 459 488 . - . ID=chr4.2;Name=chr4:54783705-54783740
+102 maf-convert match_part 459 488 120 - . Target=chr4 54783705 54783740;Name=chr4:54783705-54783740;Parent=chr4.2
+102 maf-convert match 457 475 . - . ID=chr5.7;Name=chr5:171574455-171574473
+102 maf-convert match_part 457 475 114 - . Target=chr5 171574455 171574473;Name=chr5:171574455-171574473;Parent=chr5.7
+102 maf-convert match 222 410 . - . ID=chr19.8;Name=chr19:1390856-1391052
+102 maf-convert match_part 222 410 954 - . Target=chr19 1390856 1391052;Name=chr19:1390856-1391052;Parent=chr19.8
+102 maf-convert match 224 246 . - . ID=chr6.3;Name=chr6:65786102-65786124
+102 maf-convert match_part 224 246 110 - . Target=chr6 65786102 65786124;Name=chr6:65786102-65786124;Parent=chr6.3
+102 maf-convert match 99 225 . - . ID=chr19.9;Name=chr19:1391117-1393331
+102 maf-convert match_part 99 178 320 - . Target=chr19 1393241 1393331;Name=chr19:1393241-1393331;Parent=chr19.9
+102 maf-convert match_part 179 225 237 - . Target=chr19 1391117 1391163;Name=chr19:1391117-1391163;Parent=chr19.9
+102 maf-convert match 90 126 . - . ID=chr3.8;Name=chr3:37588377-37588414
+102 maf-convert match_part 90 126 117 - . Target=chr3 37588377 37588414;Name=chr3:37588377-37588414;Parent=chr3.8
+102 maf-convert match 103 121 . - . ID=chr20.2;Name=chr20:17684745-17684763
+102 maf-convert match_part 103 121 114 - . Target=chr20 17684745 17684763;Name=chr20:17684745-17684763;Parent=chr20.2
+102 maf-convert match 88 113 . - . ID=chr16.1;Name=chr16:722484-722513
+102 maf-convert match_part 88 113 116 - . Target=chr16 722484 722513;Name=chr16:722484-722513;Parent=chr16.1
+102 maf-convert match 4 102 . - . ID=chr19.10;Name=chr19:1395388-1395484
+102 maf-convert match_part 4 102 291 - . Target=chr19 1395388 1395484;Name=chr19:1395388-1395484;Parent=chr19.10
+102 maf-convert match 69 95 . - . ID=chr22.3;Name=chr22:20726589-20726617
+102 maf-convert match_part 69 95 115 - . Target=chr22 20726589 20726617;Name=chr22:20726589-20726617;Parent=chr22.3
+##gff-version 3
chrUn_KI270748v1 maf-convert match 13905 15715 3177.2 + . Target=UN-L1MA6_pol#LINE/L1 658 1273;Name=UN-L1MA6_pol#LINE/L1:658-1273
chrUn_KI270748v1 maf-convert match 3860 4540 1775.7 + . Target=UN-L1PA2_pol#LINE/L1 1049 1275;Name=UN-L1PA2_pol#LINE/L1:1049-1275
chrUn_KI270748v1 maf-convert match 2577 3661 1607.4 - . Target=UN-L1MA6_pol#LINE/L1 518 879;Name=UN-L1MA6_pol#LINE/L1:518-879
chrUn_KI270748v1 maf-convert match 89272 90089 1559.7 - . Target=UN-L1MA6_pol#LINE/L1 884 1164;Name=UN-L1MA6_pol#LINE/L1:884-1164
chrUn_KI270748v1 maf-convert match 17572 18588 1508.0 + . Target=UN-L1PA16_pol#LINE/L1 527 864;Name=UN-L1PA16_pol#LINE/L1:527-864
+102 6 28 chr5 0 + 6 6 0 1 22 0
+102 10 29 chr5 0 + 10 10 0 1 19 0
+102 87 112 chr3 0 + 87 87 0 1 25 0
+102 91 118 chr2 0 + 91 91 0 1 27 0
+102 140 159 chr1 0 + 140 140 0 1 19 0
+102 256 277 chr18 0 + 256 256 0 1 21 0
+102 371 403 chr19 0 + 371 371 0 1 32 0
+102 425 465 chr8 0 + 425 425 0 1 40 0
+102 433 454 chr4 0 + 433 433 0 1 21 0
+102 442 463 chr20 0 + 442 442 0 1 21 0
+102 442 463 chr3 0 + 442 442 0 1 21 0
+102 442 463 chr7 0 + 442 442 0 1 21 0
+102 458 490 chr1 0 + 458 458 0 1 32 0
+102 459 490 chr18 0 + 459 459 0 1 31 0
+102 464 494 chr17 0 + 464 464 0 1 30 0
+102 467 504 chr1 0 + 467 467 0 1 37 0
+102 467 491 chr15 0 + 467 467 0 1 24 0
+102 470 489 chr13 0 + 470 470 0 1 19 0
+102 470 489 chr17 0 + 470 470 0 1 19 0
+102 470 489 chr17 0 + 470 470 0 1 19 0
+102 470 489 chr22 0 + 470 470 0 1 19 0
+102 472 499 chr10 0 + 472 472 0 1 27 0
+102 472 491 chr5 0 + 472 472 0 1 19 0
+102 476 499 chr11 0 + 476 476 0 1 23 0
+102 479 508 chr14 0 + 479 479 0 1 29 0
+102 485 508 chr3 0 + 485 485 0 1 23 0
+102 487 512 chr5 0 + 487 487 0 1 25 0
+102 493 515 chr7 0 + 493 493 0 1 22 0
+102 508 533 chr5 0 + 508 508 0 1 25 0
+102 546 565 chr17 0 + 546 546 0 1 19 0
+102 618 638 chr10 0 + 618 618 0 1 20 0
+102 640 667 chr14 0 + 640 640 0 1 27 0
+102 666 693 chr21 0 + 666 666 0 1 27 0
+102 673 696 chr3 0 + 673 673 0 1 23 0
+102 680 699 chrX 0 + 680 680 0 1 19 0
+102 635 657 chr22 0 - 635 635 0 1 22 0
+102 625 646 chr19 0 - 625 625 0 1 21 0
+102 613 645 chr19 0 - 613 613 0 1 32 0
+102 604 637 chr10 0 - 604 604 0 1 33 0
+102 574 616 chr19 0 - 574 574 0 1 42 0
+102 506 575 chr19 0 - 506 506 0 1 69 0
+102 540 563 chr5 0 - 540 540 0 1 23 0
+102 509 533 chr15 0 - 509 509 0 1 24 0
+102 500 526 chr2 0 - 500 500 0 1 26 0
+102 502 526 chr3 0 - 502 502 0 1 24 0
+102 485 524 chr1 0 - 485 485 0 1 39 0
+102 483 524 chr7 0 - 483 483 0 1 41 0
+102 502 521 chr3 0 - 502 502 0 1 19 0
+102 485 510 chr3 0 - 485 485 0 1 25 0
+102 401 509 chr19 0 - 401 401 0 1 108 0
+102 484 509 chr8 0 - 484 484 0 1 25 0
+102 484 508 chr6 0 - 484 484 0 1 24 0
+102 488 507 chr12 0 - 488 488 0 1 19 0
+102 480 505 chr19 0 - 480 480 0 1 25 0
+102 484 503 chr21 0 - 484 484 0 1 19 0
+102 477 496 chr17 0 - 477 477 0 1 19 0
+102 457 491 chr7 0 - 457 457 0 1 34 0
+102 458 490 chr12 0 - 458 458 0 1 32 0
+102 470 489 chr17 0 - 470 470 0 1 19 0
+102 470 489 chr17 0 - 470 470 0 1 19 0
+102 470 489 chr6 0 - 470 470 0 1 19 0
+102 470 489 chr7 0 - 470 470 0 1 19 0
+102 470 489 chrX 0 - 470 470 0 1 19 0
+102 458 488 chr4 0 - 458 458 0 1 30 0
+102 456 475 chr5 0 - 456 456 0 1 19 0
+102 221 410 chr19 0 - 221 221 0 1 189 0
+102 223 246 chr6 0 - 223 223 0 1 23 0
+102 98 225 chr19 0 - 98 98 0 2 80,47 0,80
+102 89 126 chr3 0 - 89 89 0 1 37 0
+102 102 121 chr20 0 - 102 102 0 1 19 0
+102 87 113 chr16 0 - 87 87 0 1 26 0
+102 3 102 chr19 0 - 3 3 0 1 99 0
+102 68 95 chr22 0 - 68 68 0 1 27 0
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@@ -11631,6 +12044,76 @@ SRR359290.9033 1 CAAAGTGCTGGGATTGCAGGCATAAGCCACTGTGCGTGGCC 41
21 2 0 0 0 0 0 0 - 102 699 223 246 chr6 170805979 65786101 65786124 1 23, 453, 65786101,
24 0 0 0 0 0 2 2 - 102 699 484 508 chr6 170805979 170257701 170257727 3 17,1,6, 191,208,209, 170257701,170257719,170257721,
23 1 0 0 0 0 1 1 - 102 699 509 533 chr15 101991189 78230485 78230510 2 20,4, 166,186, 78230485,78230506,
+23 0 0 0 0 0 0 0 + chr3 198295559 23607556 23607579 102 699 673 696 1 23, 23607556, 673,
+28 1 0 0 2 2 0 0 + chr14 107043718 104715672 104715703 102 699 479 508 3 23,2,4, 104715672,104715696,104715699, 479,502,504,
+25 0 0 0 0 0 1 2 + chr2 242193529 240456631 240456656 102 699 91 118 2 19,6, 240456631,240456650, 91,112,
+22 1 0 0 0 0 0 0 + chr11 135086622 67464146 67464169 102 699 476 499 1 23, 67464146, 476,
+36 1 0 0 3 15 0 0 + chr1 248956422 21590630 21590682 102 699 467 504 4 13,6,1,17, 21590630,21590645,21590657,21590665, 467,480,486,487,
+45 1 0 0 1 1468334 2 120 + chr10 133797422 122813034 124281414 102 699 472 638 3 17,9,20, 122813034,122813051,124281394, 472,490,618,
+31 1 0 0 2 6 0 0 + chr1 248956422 161050905 161050943 102 699 458 490 3 10,2,20, 161050905,161050918,161050923, 458,468,470,
+21 1 0 0 0 0 0 0 + chr5 181538259 93489542 93489564 102 699 6 28 1 22, 93489542, 6,
+25 2 0 0 0 0 0 0 + chr14 107043718 80332129 80332156 102 699 640 667 1 27, 80332129, 640,
+23 1 0 0 0 0 0 0 + chr15 101991189 45614749 45614773 102 699 467 491 1 24, 45614749, 467,
+38 1 0 0 3 12 1 1 + chr8 145138636 76840858 76840909 102 699 425 465 5 16,5,6,5,7, 76840858,76840875,76840887,76840897,76840902, 425,441,446,452,458,
+25 0 0 0 2 2 0 0 + chr3 198295559 152862893 152862920 102 699 87 112 3 16,3,6, 152862893,152862910,152862914, 87,103,106,
+19 0 0 0 0 0 0 0 + chr1 248956422 145870017 145870036 102 699 140 159 1 19, 145870017, 140,
+19 0 0 0 0 0 0 0 + chr5 181538259 4867425 4867444 102 699 472 491 1 19, 4867425, 472,
+19 0 0 0 0 0 0 0 + chr5 181538259 74376577 74376596 102 699 10 29 1 19, 74376577, 10,
+21 1 0 0 0 0 0 0 + chr7 159345973 157969523 157969545 102 699 493 515 1 22, 157969523, 493,
+19 0 0 0 0 0 0 0 + chr13 114364328 113342215 113342234 102 699 470 489 1 19, 113342215, 470,
+19 0 0 0 0 0 0 0 + chr17 83257441 19079609 19079628 102 699 470 489 1 19, 19079609, 470,
+38 0 0 0 1 8587829 1 57 + chr17 83257441 19205791 27793658 102 699 470 565 2 19,19, 19205791,27793639, 470,546,
+30 1 0 0 2 6 0 0 + chr18 80373285 8561208 8561245 102 699 459 490 3 6,2,23, 8561208,8561215,8561222, 459,465,467,
+26 1 0 0 2 2 0 0 + chr21 46709983 14291180 14291209 102 699 666 693 3 18,1,8, 14291180,14291199,14291201, 666,684,685,
+19 0 0 0 0 0 0 0 + chr22 50818468 23657490 23657509 102 699 470 489 1 19, 23657490, 470,
+19 0 0 0 0 0 0 0 + chrX 156040895 83302601 83302620 102 699 680 699 1 19, 83302601, 680,
+23 0 0 0 0 0 1 2 + chr5 181538259 173701199 173701222 102 699 508 533 2 16,7, 173701199,173701215, 508,526,
+23 0 0 0 1 4 0 0 + chr3 198295559 127741375 127741402 102 699 485 508 2 5,18, 127741375,127741384, 485,490,
+20 1 0 0 0 0 0 0 + chr4 190214555 3839062 3839083 102 699 433 454 1 21, 3839062, 433,
+20 1 0 0 0 0 0 0 + chr18 80373285 55335092 55335113 102 699 256 277 1 21, 55335092, 256,
+25 1 0 0 0 0 1 4 + chr17 83257441 28925929 28925955 102 699 464 494 2 9,17, 28925929,28925938, 464,477,
+20 1 0 0 0 0 0 0 + chr3 198295559 186865651 186865672 102 699 442 463 1 21, 186865651, 442,
+25 0 0 0 2 4 0 0 + chr5 181538259 169763615 169763644 102 699 487 512 3 16,1,8, 169763615,169763634,169763636, 487,503,504,
+20 1 0 0 0 0 0 0 + chr7 159345973 65260306 65260327 102 699 442 463 1 21, 65260306, 442,
+30 2 0 0 2 4 0 0 + chr19 58617616 47072201 47072237 102 699 371 403 3 3,21,8, 47072201,47072205,47072229, 371,374,395,
+20 1 0 0 0 0 0 0 + chr20 64444167 4034147 4034168 102 699 442 463 1 21, 4034147, 442,
+184 2 0 0 5 11 1 3 - chr19 58617616 1390855 1391052 102 699 221 410 7 9,21,56,4,88,3,5, 57226564,57226574,57226595,57226653,57226659,57226749,57226756, 221,230,254,310,314,402,405,
+102 4 0 0 1 3 2 2 - chr19 58617616 1388829 1388938 102 699 401 509 4 41,38,5,22, 57228678,57228719,57228757,57228765, 401,443,482,487,
+67 0 0 0 2 3 2 2 - chr19 58617616 1388523 1388593 102 699 506 575 5 13,7,3,31,13, 57229023,57229037,57229046,57229049,57229080, 506,519,526,530,562,
+77 3 0 0 5 11 0 0 - chr19 58617616 1393240 1393331 102 699 98 178 6 5,3,24,9,2,37, 57224285,57224291,57224296,57224324,57224336,57224339, 98,103,106,130,139,141,
+171 5 0 0 7 7501 7 437 - chr19 58617616 1387807 1395484 102 699 3 616 13 20,1,9,1,8,14,7,30,9,30,7,27,13, 57222132,57222154,57222155,57222164,57222167,57222176,57222192,57222199,57226453,57226463,57226493,57229769,57229796, 3,23,31,41,42,50,64,72,178,187,218,574,603,
+31 1 0 0 0 0 0 0 - chr19 58617616 1383910 1383942 102 699 613 645 1 32, 57233674, 613,
+37 2 0 0 2 2 1 2 - chr7 159345973 101590379 101590420 102 699 483 524 4 8,18,4,9, 57755553,57755561,57755580,57755585, 483,493,511,515,
+32 0 0 0 3 7 0 0 - chr12 133275309 71544986 71545025 102 699 458 490 4 10,2,17,3, 61730284,61730297,61730302,61730320, 458,468,470,487,
+21 0 0 0 0 0 0 0 - chr19 58617616 17615430 17615451 102 699 625 646 1 21, 41002165, 625,
+25 0 0 0 1 4 0 0 - chr19 58617616 18430559 18430588 102 699 480 505 2 18,7, 40187028,40187050, 480,498,
+25 0 0 0 1 5 0 0 - chr8 145138636 98433261 98433291 102 699 484 509 2 18,7, 46705345,46705368, 484,502,
+29 1 0 0 2 6 0 0 - chr4 190214555 54783704 54783740 102 699 458 488 3 7,1,22, 135430815,135430823,135430829, 458,465,466,
+24 1 0 0 1 1 0 0 - chr3 198295559 130609408 130609434 102 699 485 510 2 6,19, 67686125,67686132, 485,491,
+33 2 0 0 2 3 1 2 - chr3 198295559 37588376 37588414 102 699 89 126 4 7,20,4,4, 160707145,160707154,160707174,160707179, 89,96,118,122,
+25 1 0 0 1 4 0 0 - chr16 90338345 722483 722513 102 699 87 113 2 5,21, 89615832,89615841, 87,92,
+25 1 0 0 1 1 0 0 - chr2 242193529 192414462 192414489 102 699 500 526 2 21,5, 49779040,49779062, 500,521,
+33 1 0 0 3 7 0 0 - chr7 159345973 101723245 101723286 102 699 457 491 4 11,2,17,4, 57622687,57622701,57622706,57622724, 457,468,470,487,
+32 1 0 0 3 8 0 0 - chr10 133797422 126932869 126932910 102 699 604 637 4 16,5,3,9, 6864512,6864531,6864539,6864544, 604,620,625,628,
+26 1 0 0 1 2 0 0 - chr22 50818468 20726588 20726617 102 699 68 95 2 23,4, 30091851,30091876, 68,91,
+21 1 0 0 0 0 0 0 - chr22 50818468 46458800 46458822 102 699 635 657 1 22, 4359646, 635,
+19 0 0 0 0 0 0 0 - chr3 198295559 89815479 89815498 102 699 502 521 1 19, 108480061, 502,
+19 0 0 0 0 0 0 0 - chr5 181538259 171574454 171574473 102 699 456 475 1 19, 9963786, 456,
+19 0 0 0 0 0 0 0 - chr6 170805979 1842831 1842850 102 699 470 489 1 19, 168963129, 470,
+19 0 0 0 0 0 0 0 - chr7 159345973 100370596 100370615 102 699 470 489 1 19, 58975358, 470,
+19 0 0 0 0 0 0 0 - chr12 133275309 19357535 19357554 102 699 488 507 1 19, 113917755, 488,
+19 0 0 0 0 0 0 0 - chr17 83257441 19172450 19172469 102 699 470 489 1 19, 64084972, 470,
+19 0 0 0 0 0 0 0 - chr17 83257441 29190069 29190088 102 699 477 496 1 19, 54067353, 477,
+19 0 0 0 0 0 0 0 - chr17 83257441 58670490 58670509 102 699 470 489 1 19, 24586932, 470,
+19 0 0 0 0 0 0 0 - chr20 64444167 17684744 17684763 102 699 102 121 1 19, 46759404, 102,
+19 0 0 0 0 0 0 0 - chr21 46709983 43027934 43027953 102 699 484 503 1 19, 3682030, 484,
+19 0 0 0 0 0 0 0 - chrX 156040895 39928416 39928435 102 699 470 489 1 19, 116112460, 470,
+22 2 0 0 0 0 0 0 - chr3 198295559 33026624 33026648 102 699 502 526 1 24, 165268911, 502,
+22 1 0 0 0 0 0 0 - chr5 181538259 177958541 177958564 102 699 540 563 1 23, 3579695, 540,
+35 2 0 0 1 3 2 2 - chr1 248956422 155997873 155997913 102 699 485 524 4 23,2,4,8, 92958509,92958535,92958537,92958541, 485,508,511,516,
+21 2 0 0 0 0 0 0 - chr6 170805979 65786101 65786124 102 699 223 246 1 23, 105019855, 223,
+24 0 0 0 2 2 0 0 - chr6 170805979 170257701 170257727 102 699 484 508 3 6,1,17, 548252,548259,548261, 484,490,491,
+23 1 0 0 1 1 0 0 - chr15 101991189 78230485 78230510 102 699 509 533 2 4,20, 23760679,23760684, 509,513,
21 1 0 0 0 0 0 0 + 102 699 6 28 chr5 181538259 93489542 93489564 1 22, 6, 93489542,
19 0 0 0 0 0 0 0 + 102 699 10 29 chr5 181538259 74376577 74376596 1 19, 10, 74376577,
25 0 0 0 0 0 2 2 + 102 699 87 112 chr3 198295559 152862893 152862920 3 16,3,6, 87,103,106, 152862893,152862910,152862914,
@@ -11730,6 +12213,11 @@ SRR359290.9033 1 CAAAGTGCTGGGATTGCAGGCATAAGCCACTGTGCGTGGCC 41
240 107 0 0 12 15 11 44 +- UN-L1MA6_pol#LINE/L1 1275 517 879 chrUn_KI270748v1 93321 2576 3661 15 10,16,12,5,4,8,13,92,15,35,11,14,24,80,8, 517,528,544,557,563,570,579,593,686,703,739,751,765,790,871, 89660,89692,89742,89780,89797,89810,89834,89873,90150,90195,90301,90335,90407,90480,90721,
180 89 0 0 7 12 7 11 +- UN-L1MA6_pol#LINE/L1 1275 883 1164 chrUn_KI270748v1 93321 89271 90089 9 7,33,40,84,4,44,37,12,8, 883,891,925,966,1054,1061,1105,1143,1156, 3232,3255,3355,3476,3730,3742,3875,3988,4026,
230 96 0 0 9 12 8 39 ++ UN-L1PA16_pol#LINE/L1 1276 526 864 chrUn_KI270748v1 93321 17571 18588 12 102,63,21,18,14,14,6,38,7,22,8,13, 526,629,693,715,735,749,766,773,812,820,843,851, 17571,17877,18066,18129,18185,18256,18300,18319,18434,18457,18524,18549,
+404 194 0 0 12 17 12 18 ++ chrUn_KI270748v1 93321 13904 15715 UN-L1MA6_pol#LINE/L1 1275 657 1273 14 59,30,16,143,13,18,19,15,43,67,48,18,75,34, 13904,14082,14173,14223,14654,14695,14749,14807,14853,14983,15185,15331,15387,15613, 657,717,747,766,910,924,944,964,980,1024,1092,1142,1163,1239,
+212 15 0 0 0 0 0 0 ++ chrUn_KI270748v1 93321 3859 4540 UN-L1PA2_pol#LINE/L1 1276 1048 1275 1 227, 3859, 1048,
+240 107 0 0 11 44 12 15 -+ chrUn_KI270748v1 93321 2576 3661 UN-L1MA6_pol#LINE/L1 1275 517 879 15 10,16,12,5,4,8,13,92,15,35,11,14,24,80,8, 89660,89692,89742,89780,89797,89810,89834,89873,90150,90195,90301,90335,90407,90480,90721, 517,528,544,557,563,570,579,593,686,703,739,751,765,790,871,
+180 89 0 0 7 11 7 12 -+ chrUn_KI270748v1 93321 89271 90089 UN-L1MA6_pol#LINE/L1 1275 883 1164 9 7,33,40,84,4,44,37,12,8, 3232,3255,3355,3476,3730,3742,3875,3988,4026, 883,891,925,966,1054,1061,1105,1143,1156,
+230 96 0 0 8 39 9 12 ++ chrUn_KI270748v1 93321 17571 18588 UN-L1PA16_pol#LINE/L1 1276 526 864 12 102,63,21,18,14,14,6,38,7,22,8,13, 17571,17877,18066,18129,18185,18256,18300,18319,18434,18457,18524,18549, 526,629,693,715,735,749,766,773,812,820,843,851,
0 16 chrM 13914 71 3=1X11=1X28=2X21=1X15=1X3= * 0 0 TCGAATTCTACCCTAACATCACACACCGCACAATCCCCTATCTAAACCTTCTTACGAGCCAAAACCTACCCCTACTCCTCCTAAACC C at A=<3CC@@CBCCC8CBAC?BBBC?BB at BCCBBBCCCCBBBCBCABCBBBCCCCBCBBAC@CCBBCCACCACCCCCCBCCACCA?B NM:i:6 AS:i:429
1 0 chrM 1544 71 14=1X9=1X12=1X9=1X1=1X5=1X4=1X9=1X4=1X1=1X6=3X * 0 0 TTATATAGAGGAGATAAGTCGTAATATGGTAAGTGTATTGGAAAGTGTATTTGGATGAACTAGAGTGTAGTTTAATATAAAGCATTT 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 NM:i:13 AS:i:420
2 0 chrM 12301 71 3H2=4X13=1X2=1X1=2X15=2X3=1X1=1X1=1X2=1X5=2X1=2X5=2X3=1X2=3X4= * 0 0 GGTTTTAAAAATTTTGGTGTAATTTTAAATAAAAGTAATAATTATGTATATTATTATAATTATTCTAACTTTGATTTTTTTAAT 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(== NM:i:24 AS:i:364
=====================================
test/maf-convert-test.sh
=====================================
@@ -19,22 +19,28 @@ maf2=bs100.maf
$r blast $maf2
$r -l120 blast frameshift-new.maf
tail -n8 frameshift-new.maf | maf-swap | $r blast
+ tail -n8 frameshift-new.maf | $r -s2 blast
$r blasttab $maf2
$r blasttab frameshift-new.maf
+ $r -s2 blasttab frameshift-new.maf
head -n999 $maf1 | $r chain
$r gff 102.maf
$r -J1e9 gff 102.maf
+ $r -J1e9 -s2 gff 102.maf
$r gff frameshift-new.maf
+ $r -J1e9 -s2 bed 102.maf
$r html -l100 $maf2
head -n999 $maf1 | $r -n html
head -n999 $maf1 | $r psl
head -n999 $maf1 | $r -p psl
$r psl $maf2
$r -j1e9 psl 102.maf
+ $r -j1e9 -s2 psl 102.maf
$r -J1e9 psl 102.maf
$r psl 90089.maf
$r psl frameshift-old.maf
$r psl frameshift-new.maf
+ $r -s1 psl frameshift-new.maf
$r -n sam $maf2
head -n999 $maf1 | $r -r 'ID:1 PL:ILLUMINA SM:x' sam
$r -d sam $maf1
=====================================
test/maf-swap-test.out
=====================================
@@ -810,7 +810,7 @@ TEST maf-swap frameshift-new.maf
# batch 0
a score=3177.2 EG2=0 E=0
s chrUn_KI270748v1 13904 1811 + 93321 CAAGGGTGCCCACTCTCAGAACTTCTATTCAACATAGTACTGGATGTCCTAGCCAGAGCAATTAGGCAAAAGAAAGaaaTAAAAGGCATGAAAATTGGAAAGGAAGAAGTTAAATTGTTTCTGTTTGCAGTTGACATGATCTTATATATAGAAAACACCAATAACTCTGCCAAAAAA---TTTAGAATTCATAAATGAATTTAGTAAAGTTGCAGGATACAATGTGAACATACAAAATTCAGTAGCATTTCTACACATCAACAACAAACTATACAAAAAAagaaatcaagaaaacaATCCTATTTATAATAGCAACAAAA---------AATACTTAGATGTAAATTTAAACAAAGAGGTGAATGATCTTTACACTGAAAACTACAAAACATTGATGAAAACAATTGAAGAAGCCACAAATAAATGGAAAGATATCTCATGTTCATGGATTGGAAAAAGTAATATGTTTGAAATGTCCATACTATCCAAAGTGATGTACATATTGAATGCAATCTCTATCAAAATTCCTATGACATTTTCCCACAGAAATAGAAAAACAACTCTCAAATCTGTATGGAATCACAAAAAACTCTGAAAAGCCAAAATAATCTTGATCGAAAAAAGCAAGGCAGGAGATATCACATTACCTGACTTCAAATTATACTACATAGCTATAGCAATCGAAACACCATGGTACTGGCATAAACGCAGACACATAGACCAATTACACAGAATAAAGAGCCCATAAATAAATCTACAT---ATTATAGTCAATTGACTTTCAACAAAGGTGCCAGGAACACA---CATGGGGAAAGAACAGTCTCTTCAAAAAATGGTGTTGAGAAAACTGAATGTCCACA------AGATTGATCTTAGGCCCTTATTTCATACCATATAAAAATATAAATTCAAAATAAGTT---AGACTTAAATGTAAGACCTAGCACTATAGAACTCCTAGAAGAAAAC---AGGGGAATAACTCCAAGACATTGGTCTGGGCAATAATATTTTATGATATGACTCTAAAGCACAGGCAAGAAAAGCAACAAAACACAAATGGAATAGCATCAACCTAAAAAGCTTCTGCGCAGCAAAAGAA---AGTCAACAGAGTGAAGTGATAACCTACAAAATGGGAGGAATTATCTGCAAACTATACATTTGATAAGAGGCTAATGTCCAAAATATCTTAGGAACTCAAACAACACAataataagaaAACAAGGAACCCTAATGAAAAATTGACAAAGGATCTAAATAGACATTTCTCAAAAGAAGACATACAAATGGCCAACAGATATATA---AAAATGCTAATTATCACTGATCATCAGAGAAATGCATATTAAAACTACAATAAAATGCCATTTCACATCCGTTAGAATGGCTGTTACAGAAAAGGCAGAAGATACCAAGTGTTGGAGAGGATGTGGAGAAAAGGAAAACCTTGTA------ATTGTTGAGAATGTAAACTATTTCAGCCATTGTAAAAGACAGTATAAGTGATTCTG---------TAAAAATAGAATTACCATATGATTCAGTAATGCTATTTCTGGGCATATATTAAAAAGATATCAAATCAGTGTGTCAATGAGTTATCTGTACTCCCATATTTATTGTAGCATTATTCACAACAGCCAAGATGTGGAATTAACTTAAGTATCCATCGACACATGAGTGGATGAAGAAAATGTGGTACACATACACAATAGAATAGTATACAACCTTAaaaaataaaaaa---aGTATCATTTGTGACAACATGAATGAACCGGGAGGACATTATACTGAGTAAAATAATCCAGGCACAGAAAGCCAGATACTGCATAATCTCACTTGTATGTGGA
-s UN-L1MA6_pol#LINE/L1 657 616 + 1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysLeu-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly
+s UN-L1MA6_pol#LINE/L1 657 616 + 1275 GlnGlyCysProLeuSerProLeuLeuPheAsnIleValLeuGluValLeuAlaArgAlaIleArgGlnGluLysGluIleLysGlyIleGlnIleGlyLysGluGluValLysLeuSerLeuPheAlaAspAspMetIleLeuTyrIleGluAsnProLysAspSerThrLysLysXaa-LeuGluLeuIleAsnGluPheSerLysValAlaGlyTyrLysIleAsnIleGlnLysSerValAlaPheLeuTyrAlaAsnSerGluLeu-SerGluLysGluIleLyslysthrilepropheThrIleAlaThrLysLysIleLys--TyrLeuGlyIleAsnLeuThrLysGluValLysAspLeuTyrXaaGluAsnTyrLysThrLeuMetLysGluIleGluGluAspThrAsnLysTrpLysAspIleProCysSerTrpIleGlyArgIleAsnIleValLysMetSerIleLeuProLysAlaIleTyrArgPheAsnAlaIleProIleLysIleProMetThrPhePheThrGluIleGluLysThrIleLeuLysPheValTrpAsnHisLysArgProArgIleAlaLysAlaIleLeuSerLysLysAsnLysAlaGlyGlyIleThrLeuProAspPheLysIleTyrTyrLysAlaIleValThrLysThrAlaTrpTyrTrpHisLysAsnArgHisIleAspGlnTrpAsnArgIleGluSerProGluIleAsnProArgIle--TyrSerGlnLeuIlePheAspLysGlyAlaLysAsnThrGln--TrpGlyLysAspSerLeuPheAsnLysTrpCysTrpGluAsnTrpIleSerThrCysArgArgMetLysLeuAspProTyrLeuSerProTyrThrLysIleAsnSerLysTrpIleLys-AspLeuAsnValArgProGluThrMetLysLeuLeuGluGluAsnIle-GlyGluMetLeuHisAspIleGlyLeuGlyLysAspPheLeuAspLysThrSerLysAlaGlnAlaThrLysAlaLysIleAspLysTrpAspTyrIleLysLeuLysSerPheCysThrAlaLysGluThr-IleAsnArgValLysArgGlnProThrGluTrpGluLysIlePheAlaAsnTyrAlaSerAspLysGlyLeuIleSerArgIleTyrLysGluLeuLysGlnLeuAsnSerLysLysThrAsnAsnProIleXaaLysTrpAlaLysAspLeuAsnArgHisPheSerLysGluAspIleGlnMetAlaAsnArgTyrMetLys-LysCysSerThrSerLeuIleIleArgGluMetGlnIleLysThrThrMetArgTyrHisLeuThrProValArgMetAlaIleIleLysLysThrLysAspAsnLysCysTrpArgGlyCysGlyGluLysGlyThrLeuThrHisCys--TrpTrpGluCysLysLeuValGlnProLeuTrpLysThrValTrpArgPheLeuLysLysLeu--LysIleGluLeuProTyrAspProAlaIleProLeuLeuGlyIleTyrProLysGluMetLysSerValCysArgArgAspIleCysThrProMetPheIleAlaAlaLeuPheThrIleAlaLysIleTrpAsnGlnProLysCysProSerThrAspGluTrpIleLysLysMetTrpTyrIleTyrThrMetGluTyrTyrSerAlaIleLysLysAsnGluIle-LeuSerPheAlaThrThrTrpMetAsnLeuGluAspIleMetLeuSerGluIleSerGlnAlaGlnLysAspLysTyrArgMetIleSerLeuIleCysGly
a score=1775.7 EG2=2.9e-164 E=1.5e-169
s chrUn_KI270748v1 3859 681 + 93321 CTAATATCCGGAATCTACAATGAACCCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACTATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTTACACCAGTTAGAATGGCCATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACATTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGACAGTGTGGTGATTCCGCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTACTGTGGCACTATTCACAATAGCAAAGACTTGGAACCAATCCAAATGTCCAACAATGATAGACTGGATTAAGAAAACGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACAATCACAAGGACAAAAAACCAAACACCGCATGTTCTCACTCATAGGTGGGAAT
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/75b5dac638dbf3553c116536e0c99ef3d1be4a97...dd2ce64cb36221acf16aba62cd64aab1142936fc
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/compare/75b5dac638dbf3553c116536e0c99ef3d1be4a97...dd2ce64cb36221acf16aba62cd64aab1142936fc
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