[med-svn] [Git][med-team/last-align][upstream] New upstream version 1609
Charles Plessy (@plessy)
gitlab at salsa.debian.org
Wed Feb 19 00:30:17 GMT 2025
Charles Plessy pushed to branch upstream at Debian Med / last-align
Commits:
dad6cfa0 by Charles Plessy at 2025-02-19T09:07:01+09:00
New upstream version 1609
- - - - -
5 changed files:
- bin/maf-convert
- src/makefile
- + test/homSap-monDom.maf
- test/maf-convert-test.out
- test/maf-convert-test.sh
Changes:
=====================================
bin/maf-convert
=====================================
@@ -679,6 +679,11 @@ def mismapProbabilityFromText(probString):
raise ValueError("bad probability: " + probString)
return p
+def smallParts(size, symbol):
+ maxSize = 268435455
+ q, r = divmod(size, maxSize)
+ return (str(maxSize) + symbol) * q + (str(r) + symbol) * (r > 0)
+
def cigarParts(alignmentColumns):
# (doesn't handle translated alignments)
# uses "read-ahead" technique, aiming to be as fast as possible:
@@ -743,7 +748,7 @@ def writeSam(readGroup, mafs):
if not isSplice: editDistance += d
else:
pos = begA
- if begB: cigar.append(str(begB) + "H")
+ cigar.append(smallParts(begB, "H"))
oldEndA = endA
alignmentColumns = list(zip(rowA.upper(), rowB.upper()))
@@ -759,8 +764,7 @@ def writeSam(readGroup, mafs):
z = zip(rowB, qFields[2])
qual += ''.join(j for i, j in z if i != "-")
- revBegB = seqLenB - endB
- if revBegB: cigar.append(str(revBegB) + "H")
+ cigar.append(smallParts(seqLenB - endB, "H"))
if strandA == "-":
seq = revcomp(seq)
=====================================
src/makefile
=====================================
@@ -95,7 +95,7 @@ ScoreMatrixData.hh: ../data/*.mat
../build/mat-inc.sh ../data/*.mat > $@
VERSION1 = git describe --dirty
-VERSION2 = echo ' (HEAD -> main, tag: 1608) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
+VERSION2 = echo ' (HEAD -> main, tag: 1609) ' | sed -e 's/.*tag: *//' -e 's/[,) ].*//'
VERSION = \"`test -e ../.git && $(VERSION1) || $(VERSION2)`\"
=====================================
test/homSap-monDom.maf
=====================================
@@ -0,0 +1,98 @@
+# LAST version 1584
+#
+# a=29 b=1 A=28 B=1 e=185 d=116 x=184 y=52 z=184 H=100 E=3.87001
+# R=01 u=2 s=2 S=1 M=0 T=0 m=10 l=1 n=10 C=2 k=1 w=1000 t=5.22312 j=3 Q=0
+# /home/mcfrith/data/genome/mammal/homSap/last/homSap-cMAM4
+# Reference sequences=195 normal letters=2934876451
+# lambda=0.207774 K=0.191089
+#
+# A C G T M S K W R Y B D H V
+# A 4 -6 -2 -6 2 -4 -4 1 2 -6 -5 1 0 1
+# C -6 6 -6 -2 2 3 -3 -4 -6 2 1 -4 1 0
+# G -2 -6 6 -6 -3 3 2 -4 2 -6 0 1 -4 1
+# T -6 -2 -6 4 -4 -4 2 1 -6 2 1 0 1 -5
+# M 2 2 -3 -4 2 0 -4 0 1 -1 -2 -1 0 1
+# S -4 3 3 -4 0 3 0 -4 0 0 1 -1 -1 1
+# K -4 -3 2 2 -4 0 2 0 -1 1 1 0 -1 -2
+# W 1 -4 -4 1 0 -4 0 1 0 0 -1 0 0 -1
+# R 2 -6 2 -6 1 0 -1 0 2 -6 -2 1 -1 1
+# Y -6 2 -6 2 -1 0 1 0 -6 2 1 -1 1 -2
+# B -5 1 0 1 -2 1 1 -1 -2 1 1 -1 0 -1
+# D 1 -4 1 0 -1 -1 0 0 1 -1 -1 0 0 0
+# H 0 1 -4 1 0 -1 -1 0 -1 1 0 0 0 -1
+# V 1 0 1 -5 1 1 -2 -1 1 -2 -1 0 -1 1
+#
+# Coordinates are 0-based. For - strand matches, coordinates
+# in the reverse complement of the 2nd sequence are used.
+#
+# name start alnSize strand seqSize alignment
+#
+# m=1 s=185
+#
+# m=1 s=185
+#
+# Query sequences=13 normal letters=3554259256
+a score=764 mismap=0.5
+s chr1 14674 379 + 248956422 GGGAAGGTGTCATGGAGCCCCCTACGATTCCCAGTCGTCCtcgtcctcctctgcctgtggctgctgcggtggcggcAGAGGAGGGATGGAGTCTGACACGCGGGCAAAGGCTCCTCCGGGCCCCTCACCA------GCCCCAGGTCCTTTCCCAGAGATGCCTGGAGGGAAAA--GGCTGAGTGAGGGTGGTtggTGGGAAACCCTGGTTCCCCCAGCCCCCGGAGACTTAAATACAGGAAGAAAAAGGCAGGACA---------GAATTACAAGGTG---CTGG---------CCCAGGGCGGGCAGCGGCCCTGCCTCCTACCCTTGCGCCTCATGACCAGCTTGTTGAAGAGATCCGACATCAAGTGCCCACCTTGGCTCGTGGCTCTCACTGCAACGGGAAAGC
+s NC_077231.1 215087875 379 - 328091318 GGTAAGGTGT----GGCTTCCCTATGACTCCCATTCATCCTCATCTTCCTCTCCAGGTGGCTGCTGCAACATTGGTAGGGGTGGAATTGAGTCTGACATGCGGGCAAAGGCTCCTCCAGGGCCTTCCCCAGTGTTtgctccaggtcctttcccagagaTGCCTAAAAGAAAAAATGTACAAGTGA-----------GGGAAGGCTAGGCTGCCTCAGCTCCAGAAAA---------AAGAAGCAAGAGGCACATTATGAATGGATGAATCATAAATTGGGCCTGGAAGGAGGCACCAAGGTCTCACTGTGACTC-----CTTACCTTTGCGCCTCATGACTAGTTTGTTGAAGAGATCTGACATTAGGTCACCACCCTGGCTTGTGGCTCTCACTGTAACAAaaaaac
+
+a score=202 mismap=1
+s chr1 19971 154 + 248956422 AGACTGGGGAGGGACAAAGGCTGCTCTGTCCTGGTGCTCCCACAAAGGAGAAGGGCTGATCACTCAAAGTTGCGAACACCAAGCTC----------AACAATGAGCCCTGGAAAATTTCTGGAATGGATTATTAAACAGAGAGTCTGTAAGCACTTAGAAAAGG
+s NC_077231.1 309006733 150 + 328091318 AGACGAGAGATGGGCAATGGCTGCCCTGACTT--------TTGAAAGGGGGAAGAGAGATCA------GTTCCGGAAACCACGGCCCTGAGAACGAGACATTAATTCCCAGCAAAATGCTAAAAGGGATTCTCAAAGAGAGGGTCTGTAAACACTCAGAAAAGG
+
+a score=193 mismap=0.8
+s chr1 20516 157 + 248956422 TAGACTGCAATCACCAAGATGAAATTTACAAGGAACAAATGTGAAGCCCAACATTTAGGTTTTAAAAATCAAGCGTATAAATACAGAAGGTGGAGGGAACTTGCTTTAGACACAGTTCAGGT-GAAGAAAGACCTGGAAACTTCTGTTAACTATAAGC
+s NC_077230.1 239963377 132 + 454668073 TGGGCTAAAATCAGAAACATGACATTTACCAGGGATTAATATAAAGTCCTACATTTAGGTTTTAAAAATTAACAGCACAAA--------------------TTCCTTAGCCATATTTCACATAGGGAAAAGATCTGGAA------GTTAATTTCAAGC
+
+a score=186 mismap=0.83
+s chr1 24083 86 + 248956422 TCTATGGCTTTGAATCCTGGCTCTGTCACTAGGCCAGGTCTCTCAGCCCTTCTGTGCCTCAGTTTCCTCATCTATAAAATGAGATG
+s NC_077229.1 223646143 86 + 538302405 TCTGTGAGTTCAAATCCAGCCTCAGACACTAGCTGAGTGACCTTGGACCTTGTTTGCTTCAGTTTCCTCATTGATAAAATGAGTTG
+
+a score=230 mismap=0.63
+s chr1 44947 138 + 248956422 CAAAAAATGCTCAACATCACTATTTGTCAGGGAAGTACTAATTAAAACCAAAATGAGATGTCCCCTCAAACCTGTTAGAATGGCTATTATCAAAAAGATGAAAGATAGCAACTATCAGAGAGGATGATAGAAAAGGGA
+s NC_077229.1 380433580 138 + 538302405 CAAAACATGCTCTAAAACACTTGTAATTGGAGAAGCACAAATTAAAACAATTCTGAGCTATCTCCTCAAATCTATCAGATTAGCTATTTTGACAGGAAAGAAAAGTGACAAAACTTTGAGGGGATATGGGAAAAGTGA
+
+a score=355 mismap=0.63
+s chr1 47567 300 + 248956422 TtttttccTTACTTTCCATCACCAAGTAACTCTTCTGATATTTTTTCTCTTGAGAAAATTAATATGACTCATAGATCTGGTTCCCAAGAGAAATCAATGGAGGCCTGGTTACAAGGATCTAAGAAGCATCAATGGGTCACTAACATCTAGTGGTACTAATTAACTCTGTTAATCATTGGGAAGAAAATGTATATATACTTTTGTCTTGGAGCTGATTCTACTAGAAAGCAGAAATCAAAATGATCAGTTTCCCAGTGT----CACTACTGCACACCCTGGAACAGAACAGGTAGGTCAGAAAAA
+s NC_077227.1 171526596 292 + 760810273 TTCtctctctctgttttATCACTAAGCAACCTTTCTAATGTTTTTCCTCTTGGGAAAACTAGTGTGACTTCAAGAAACAATTACCAAGGGAATTAATCATAAGCTAGGTATTAGAAGTCTAAGAAGCATCATTGGGTCACTGACAGTCAGAGCAACTAAGTATGTTGCTTTCTCTTAGGGAAGAACTTAGTTTAACTTTTTTTCTTTAGAGGTTATTAAATTACATTTCTGAATT------------TTTCTCATTCTTAAATACAATTTCATATTCTGTGATAGAACAGGTAGGTGAGAGGAA
+
+a score=410 mismap=0.63
+s chr1 48769 245 + 248956422 TTAGAGAAATGCAAATCAAAACCATATTGAGATATCATCTCATACCAGGCAGAATGGCTATTAT--TAAAAAGTCAAAAATAACAGATATCGGTGAGGTTACAGAGAAAAGGGAACACTTATACACTGTTGGTGGGACTGTAAATTATTTCAACCATTGTGGAAAGCAGTATGGGATGGCGATTCCTCAAAAAGCCAAAAACAGAACTATCATTCAACCCAGCAATTCCATTACTGGGTATATACCC
+s NC_077227.1 432674215 232 + 760810273 TTAGACAAATACAAATCAAAACAATTCTGAGATATCATCTTATACCAGAC----TGGCTAAAATGATAAAAGGGCaaaaatggcaaaTCTTGGAGGGGATGTAGAAAAATGGAAATACTAATATACTGTTGGTGGAACTAGAACCTAATGTAACCATTTTGGAGAACAATTTGGAATTATGATCAGTTAAAAAACTGA----------TCCCTTAGACTTAGCAATT-CACTATTGGGTTTGTTTCC
+
+a score=2697 mismap=0.01
+s chr1 62902 978 + 248956422 TCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTttttctcttcttctcttTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAA---AGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGAC
+s NC_077227.1 171564230 981 + 760810273 TCTTTACCCTTAGGTCATTTTAGCAACTGTGGAACCAACTGAGTCAATGGATGGAGTAAATAATTCTGTGGTAAATGAGTTTGTCCTTTTGGGTCTCTCTGCTTCTTGGGAGATGAAGATTCTACTcttttttttcttctctgtgttttttgtgGGAATCATGTTTGGAAACctcttcattgtattcactgtgatttttgACCCTCATTTACACTCCCCCATGTATTTCTTGTTGGCCAATCTTTCTCTCATTGACCTGGGTCTGTCTGCTACCACAGTACCAAGGATGATAGTGGACCTTTTCAGTGAATGTAATATAGTCATCTCCTTCCCAGGTTGCATGACACAGATGTTCTTTATCCATGTCATGGGAGGAACTGAGATGGTTCTGCTCATAGTCATGGCATATGACAGATATACAGCAATTTGTAAGCCTCTCCACTATTTGACAATTATGAATCCAAAAATGTGTATTTGCTTTGTAGTGACTGCCTGGATAGTTGGAGTGATCCATGCGATCTCTCAGTTTGTTTTTGTTATAAATTTGCCTTTCTGTGGTCCAAATAAAGTGGAGAGCTTTTATTGTGACTTTCCTCGGGTCATAAAACTTGCGTGCATAGACACCTATAGCCTGGAGTTTGTGGTTATAGCCAATAGTGGTTTTATCTCCATTGGGACTTTTTTCCTATTGATTATCTCCTACATTTTCATCCTGGCCTCTGTTCGACAACATTCTGTCGGTGATTTGTCCAAAGCCTTCTTTACTTTGTCAGCTCACATCACTGTGGTGATTTTATTTTTTGGTCCATGCATGTTTCTTTATGTGTGGCCATTTCCTACATTGTCACTTGATAAATTCTTTGCTATTGTTGACTTTGTTGTCACCCCTGTCTTGAATCCTGCTATCTATACATTAAGGAACAAGGATATGAAGATGGCAATGAGGAGACTGAGCAGCCAGATTGTGAGTTCTAGGGAGAC
+
+a score=601 mismap=0.64
+s chr1 69075 254 + 248956422 GAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACT---CTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAG
+s NC_077227.1 171835366 257 + 760810273 GAGATGAATAACTCTATGGTGAATGAATTCATTTTGTTGGGACTCACCAATTCTTGGGAACTTGAGATTTTCTTTTTtgtggttttctttCTGGCCTATACATTAATCTTGACTGGGAACTTTCTCATTATACTCATGGTGACTCTTGACTCCCATCTGCATTCAACCCCCATGTACTTCCTCCTGGCCAACCTCTCTCTTTTTGACATGTCTCTTTCCACTGTTACTGTCCCCAAAATGATCATAGACTTCTTCAG
+
+a score=612 mismap=0.5
+s chr1 186298 190 + 248956422 GCTCCAGGGCCCG--CTCACCTTGCTCctgctccttctgcttcttcttctccAGCTTTCGCTCCTTCATGCTGCGCAGCTTGGCCTTGCCGATGCCCCCAGCTTGGCGGATGGACTCTAGCAGAGTGGCCCGGCCACCGGAGGGGTCGACCACTTCCCTGGGAGCTCCCTGGACTGGAGCCAGGAGGTGGGG
+s NC_077231.1 215094373 192 - 328091318 GCTCTAAGGGCAGGCTTTACCTTGTTcctgttccttctgcttcttcttctcCAGTTTTCGCTCCTTCACACTTCTTAGCTTAGCCTTGCCAATACCTCCTGCCTGGCGGATTGACTCTAGCAAGGTTGCCCGTCCACTGGAAGGATCCACAACTTCCTTGGGCGGTACATGAACTGGAACTAAGaggggggg
+
+a score=239 mismap=0.51
+s chr1 190586 251 + 248956422 GAGCCCTGGAAAATTTCTGGAATGGATTATTAAACAGAGAGTCTGTAAGCACTTAGAAAAGGCCGCGGTGAGTCCCAGGGGCCAGCACTGCTCGAAATGTACAGCATTTCTCTTTGTAACAGGATTATTAGCCTGCTGTGCCCGGGGAAAACATGCAGCACAGTGCATCTC--------------GAGTCAGCAGGATTTTGACGGCTTCTAACAAAATCTTGTAGACAAGATGGAGCTATGGGGGTTGGAGGACAGAACATATA
+s NC_077229.1 448805062 244 + 538302405 GATTCCTCATAAAACTCTAGAATGTATTATTAAACAGAAGGTCAGTGAACATCTAGAAAAGGGAGCTGTGAATGAAAGGGGCCAGACTAGCTTCATTTtctttctttttctttttttGACAAGCTTATTAG-------------------ACTTGCAGAAAAATAGAATTCTTTAGTTATAATTTCAGTCAGAAATTTGAAAAAGCCTCCTGCT--ACTCTTGTGGACAAGATGGAGACCTGAGAGCTAGCTGATAGGGCATTTA
+
+a score=212 mismap=0.5
+s chr1 191039 216 + 248956422 TAGACTGCAATCACCAAGATGAAATTTACAAGGAACAAATGTGAAGCCCAACATTTAGGTTTTAAAAATCAAGCGTATAAATACAGAAGGTGGAGGGAACTTGCTTTAGACACAGTTCAGGTGAAGAAAGACCTGGAAACTTCTGTTAACTA----------TAAGCTCAGTAGGGGCTAAAAG---CATGTTAATCGGCATAAAAAGGCAATGAGATCTTAGGGTACA
+s NC_077228.1 350296867 215 - 544688058 TAGGCTGTATCTACAAAGATGCAACTTAATAGGAATGAATGCAAAGTTCAGCACTTGGGGTAAAAATATCAACCTTACACATGAAGAGAATTGGGAAAACATGCCTGGGTGATAGTTTATGTGAAAAGAA--------------GTTAGCTAAAACGGGATGGAAGCACAATATGAGTTCACAGTGACATAATAGACAaaaaaaaaaGCTAATTCAACCTTGGGTTACA
+
+a score=230 mismap=0.79
+s chr1 194612 83 + 248956422 TGGCTTTGAATCCTGGCTCTGTCACT--------AGGCCAGGTCTCTCAGCCTTTCTGTGCCTCAGTTTCCTCATCTATAAAATGAGATGA
+s NC_077235.1 42909095 91 + 89414197 TGGTTTCCAATCCTGGCTTTGTCACTTATTCCCAAGATCAGATCACTCAAATTTTCTGTGCCTTTGTTTCTTAATCTAAAAAATGAGATGA
+
+a score=189 mismap=0.69
+s chr1 200108 76 + 248956422 CCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCT-CTTCCCAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCC
+s NC_077232.1 103349947 77 + 311077132 CCGGCCCCACCCAGGCTGCCTGCTCTGCTGGCCCTGCTTGTCTGAGCTCCGGCTCTTGCCCCGGCCCTGCCCACCCC
+
+a score=268 mismap=1
+s chr1 394428 109 + 248956422 ACCCTCTCACTGGAATGTAAACTCCCTGAAAGCAAGGAC--TTGGCTTATTGCTGTATCCCAAGAGCCTGACACAGTGCCTGGCACATGGTAGACACTCAATAGATGTTTG
+s NC_077227.1 24094667 111 + 760810273 ACCATGCTACTCCAATGTAAACTCCCTGAAAGCAGGGACTATTTTGTTGTCACAGTATCCCCAGTACCTAGCccagtgcctggcACATAGTAGGCACTTACTAAATGCATG
+
+a score=269 mismap=1
+s chr1 403533 100 + 248956422 AAAAATCAGAGCTAAAGATAC-TTAAACACTACAGTTAAAATGCCATGGTTGTCTATTGGCTTAATGAATTCTCTTATGAAATCAACTCTAAAATGTTATC
+s NC_077230.1 104187276 101 + 454668073 AAAAATCAGAACTGAAGTTACCTTAGACACTACAGTAAAAATGTTGAGATAATATATTGGTCTAATGATTTCTTTTATGAACTCAATTCTAAAATGTTATC
+
=====================================
test/maf-convert-test.out
=====================================
@@ -23617,6 +23617,24 @@ chr15 16 L1PA3_3end#LINE/L1 467 84 84955187H52=1X10=1X83=1X13=1X3=1X23=1X54=1X47
chr15 0 L1PA3_3end#LINE/L1 40 81 17042713H2=1X3=1X7=1X6=1X12=1X14=1X16=1X1=2X78=1X8=1X7=1X11=1X64=2X2=1X5=1X13=1X10=1X35=1X39=1X59=1X6=1X15=1X35=1X12=1X64=1X41=1X7=1X4=1X27=1X43=2X3=1X23=1X2=1X2=1D2=1X1=1X12=2X18=1X11=1X10=1X7=1X3=1X12=1X58=84947620H * 0 0 aaaaaacaaacaaataaCCCCTTCAAAAAGTGGGTGAAGGACATGAACATACACTTCTCAAAAGAATATGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAAATACCATCACACACCAATTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACAAAGTGGGTGGCACTGTAAACTAGTACAACCATTGTAGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACCAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATGTACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTAGTCACAATAGCAAAGAGTTGGAACCAACCCAAATGTCCAACAATGATAGACTTGATTAAGAAAATATGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGTGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATTGCAAGAATAAAAGACCAAACACCGCATATTCTCACTCATAAGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAATGTCATACTCTGGGGACTGTTGTGGGGTGTGGTGAGGCGCAGGGATAGCATTATGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAGCGTGGTACATGTATACATGTGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata * NM:i:47 AS:i:4053
chr15 16 L1PA2_3end#LINE/L1 41 73 84941003H33=1X112=1X4=1X45=1X115=1X85=1X11=1X50=2X24=1X40=1X19=1X13=1X6=1X12=1X8=1X7=1D21=1X86=1X3=1X15=1X3=1X11=1X19=1X17=1X23=1X45=17049334H * 0 0 AGAaaaaaacaAACAACCCCATCAAAAAGTGGGTGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGTGATATCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACTACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTGGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACATATGTTTATTGTGGCATTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAACCATAGACTGGATTAAGAAAATGTGGTACATATACACCATGGAATACTATGCAGCCATAAAAAATGAAGAGTTCATGTCCTTTGTAGAGACATGGATGAAACTGGAAACCATCATTCTCAGCAAACTATCACAAGAACAAAAACCAAACACCGCATATTTTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTGGGGGCAGGAGGGAGGGATAGCATTAGGAAATATACCTAATACTAGATGACGAGTTAGTGGCTGCAGCGCACCAGCATGTCACATGTATACATATGTAACTAATCTGCACAATGTGCACATGTACCCTAAAACTTAAAGTATAATAAAA * NM:i:26 AS:i:4305
chr15 16 L1P1_orf2#LINE/L1 2609 100 84940427H4=1X17=1X92=1X22=1X25=1X103=1X20=1X45=1X3=1X39=1X28=1X14=1X70=1X16=1X63=17050187H * 0 0 TCACACTACCTGACTTCAAACTGTACTACAAGGCtacagtaaccaaaacagCATGGTACTGGTACCAAAACAGAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAACACCGCATATCTACAACTATCTGACCTTTGACAAACCTGAGAAAAACAAGAAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAAGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATAGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAAAATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTAC * NM:i:14 AS:i:2956
+ at HD VN:1.3 SO:unsorted
+ at PG ID:lastal PN:lastal VN:1584
+NC_077231.1 16 chr1 14675 3 215087875H2=1X7=4D1=4X5=1X2=1X5=1X2=1X5=1X2=1X6=1X1=2X11=6X2=1X2=1X2=1X2=1X2=1X10=1X18=1X2=1X2=1X2=1X3=6I2=1X24=2X1=1X1=1X4=2I1=4X5=11D5=2X1=2X2=1X1=1X2=1X4=1X2=1X1=1X1=1X1=9D1=1X4=1X2=1X5=4X1=9I4=1X1=1X2=2X2=3I4=9I2=1X3=1X1=3X1=1X1=1X1=1X1=1X1=5D1=1X4=1X14=1X2=1X14=1X5=1X1=1X2=2X5=1X5=1X13=1X3=3X3=1X1=113003064H * 0 0 GGTAAGGTGTGGCTTCCCTATGACTCCCATTCATCCTCATCTTCCTCTCCAGGTGGCTGCTGCAACATTGGTAGGGGTGGAATTGAGTCTGACATGCGGGCAAAGGCTCCTCCAGGGCCTTCCCCAGTGTTtgctccaggtcctttcccagagaTGCCTAAAAGAAAAAATGTACAAGTGAGGGAAGGCTAGGCTGCCTCAGCTCCAGAAAAAAGAAGCAAGAGGCACATTATGAATGGATGAATCATAAATTGGGCCTGGAAGGAGGCACCAAGGTCTCACTGTGACTCCTTACCTTTGCGCCTCATGACTAGTTTGTTGAAGAGATCTGACATTAGGTCACCACCCTGGCTTGTGGCTCTCACTGTAACAAaaaaac * NM:i:144 AS:i:764
+NC_077231.1 0 chr1 19972 0 268435455H40571278H4=2X1=1X2=1X2=1X3=1X6=1X3=1X1=1X1=8D3X5=1X1=1X1=1X1=3X5=6D3=1X2=1X1=1X4=1X1=2X1=10I1X3=1X1=1X1=2X2=2X1=1X3=1X1=1X2=2X2=1X5=1X1=1X3=1X4=1X8=1X4=1X8=19084435H * 0 0 AGACGAGAGATGGGCAATGGCTGCCCTGACTTTTGAAAGGGGGAAGAGAGATCAGTTCCGGAAACCACGGCCCTGAGAACGAGACATTAATTCCCAGCAAAATGCTAAAAGGGATTCTCAAAGAGAGGGTCTGTAAACACTCAGAAAAGG * NM:i:67 AS:i:202
+NC_077230.1 0 chr1 20517 1 239963377H1=1X1=1X2=2X5=2X2=1X4=1X6=1X3=1X1=2X3=1X1=1X3=1X2=1X19=1X2=2X1=1X1=1X3=20D1=1X1=1X4=1X2=1X1=1X4=2X1=1I1=3X5=1X6=6D5=1X1=2X4=214704564H * 0 0 TGGGCTAAAATCAGAAACATGACATTTACCAGGGATTAATATAAAGTCCTACATTTAGGTTTTAAAAATTAACAGCACAAATTCCTTAGCCATATTTCACATAGGGAAAAGATCTGGAAGTTAATTTCAAGC * NM:i:62 AS:i:193
+NC_077229.1 0 chr1 24084 1 223646143H3=1X2=2X2=2X5=1X1=1X3=1X1=1X6=3X2=4X2=2X1=1X4=1X1=1X3=1X13=2X10=1X2=268435455H46220721H * 0 0 TCTGTGAGTTCAAATCCAGCCTCAGACACTAGCTGAGTGACCTTGGACCTTGTTTGCTTCAGTTTCCTCATTGATAAAATGAGTTG * NM:i:25 AS:i:186
+NC_077229.1 0 chr1 44948 2 268435455H111998125H5=1X6=1X1=1X1=1X4=2X1=2X1=2X1=1X4=1X2=1X9=1X1=3X4=1X1=1X2=1X7=1X2=1X1=1X3=1X1=1X6=1X1=1X1=1X1=3X1=1X4=2X1=2X3=3X1=2X3=1X4=4X6=1X2=157868687H * 0 0 CAAAACATGCTCTAAAACACTTGTAATTGGAGAAGCACAAATTAAAACAATTCTGAGCTATCTCCTCAAATCTATCAGATTAGCTATTTTGACAGGAAAGAAAAGTGACAAAACTTTGAGGGGATATGGGAAAAGTGA * NM:i:47 AS:i:230
+NC_077227.1 0 chr1 47568 2 171526596H2=1X1=1X2=2X1=3X2=2X5=1X3=1X3=2X4=1X2=1X5=1X6=1X5=1X2=1X1=1X5=3X3=5X2=1X5=1X3=1X1=1X1=4X1=1X2=2X3=3X1=4X14=1X9=1X3=3X2=1X1=2X5=1X2=2X1=3X2=2X2=1X1=1X8=2X1=3X1=2X1=3X4=3X2=1X3=1X1=1X3=2X1=1X2=1X1=3X1=1X3=1X1=12D4=1X2=1X1=1X1=4I1X2=1X1=1X1=1X2=1X1=2X3=2X1=1X13=1X3=2X2=268435455H268435455H52412475H * 0 0 TTCtctctctctgttttATCACTAAGCAACCTTTCTAATGTTTTTCCTCTTGGGAAAACTAGTGTGACTTCAAGAAACAATTACCAAGGGAATTAATCATAAGCTAGGTATTAGAAGTCTAAGAAGCATCATTGGGTCACTGACAGTCAGAGCAACTAAGTATGTTGCTTTCTCTTAGGGAAGAACTTAGTTTAACTTTTTTTCTTTAGAGGTTATTAAATTACATTTCTGAATTTTTCTCATTCTTAAATACAATTTCATATTCTGTGATAGAACAGGTAGGTGAGAGGAA * NM:i:121 AS:i:355
+NC_077227.1 0 chr1 48770 2 268435455H164238760H5=1X4=1X11=1X2=2X13=1X7=1X1=4D6=2X2=2I5=1X1=1X7=2X2=1X2=1X1=1X2=1X1=1X2=1X1=2X3=1X3=1X2=1X2=1X3=1X3=1X11=1X3=2X2=2X2=1X1=2X7=1X4=1X1=1X2=1X1=1X3=1X2=3X3=3X1=1X5=1X1=2X1=10D2X1=1X2=2X2=2X7=1D2=1X2=1X5=1X1=1X1=2X2=268435455H59700371H * 0 0 TTAGACAAATACAAATCAAAACAATTCTGAGATATCATCTTATACCAGACTGGCTAAAATGATAAAAGGGCaaaaatggcaaaTCTTGGAGGGGATGTAGAAAAATGGAAATACTAATATACTGTTGGTGGAACTAGAACCTAATGTAACCATTTTGGAGAACAATTTGGAATTATGATCAGTTAAAAAACTGATCCCTTAGACTTAGCAATTCACTATTGGGTTTGTTTCC * NM:i:81 AS:i:410
+NC_077227.1 0 chr1 62903 20 171564230H2=1X2=1X1=2X1=1X4=3X2=1X2=3X2=6X1=1X1=1X4=1X3=1X4=3X7=1X1=1X3=1X6=2X2=1X5=2X1=2X1=1X2=1X2=2X1=4X2=1X1=1X3=1X3=1X2=1X2=1X1=1X2=1X3=1X1=1X9=1X1=1X2=1X1=1X9=1X2=2X1=1X5=1X11=1X5=1X5=1X5=1X5=1X18=1X1=2X2=1X7=1X2=1X2=1X9=1X2=1X1=1X2=1X2=2X10=1X2=1X3=1X4=4X2=1X5=1X1=1X3=1X5=3I3=1X2=1X7=4X8=1X3=1X1=1X15=1X9=2X3=1X5=1X5=1X17=1X2=1X2=1X2=1X2=1X2=1X2=1X15=3X2=1X11=1X8=1X2=1X1=2X2=1X4=3X1=1X2=1X3=1X1=2X4=1X5=1X5=1X2=1X17=1X8=1X2=1X8=1X2=1X5=1X4=1X15=1X11=1X2=1X8=1X5=1X5=1X3=1X1=1X2=1X2=1X8=1X1=2X5=1X5=1X2=1X2=1X2=1X2=1X2=1X2=1X2=1X2=2X1=1X2=1X3=1X1=1X2=1X8=1X2=1X4=1X1=1X4=1X1=1X2=1X6=6X6=1X8=1X5=1X4=1X3=1X11=1X2=1X3=1X4=1X7=1X15=1X2=1X8=1X2=1X5=3X4=1X1=1X8=1X5=1X2=2X1=2X20=1X1=1X8=1X8=1X11=1X9=1X1=1X8=1X2=1X4=5X2=1X3=1X1=1X1=1X5=1X6=268435455H268435455H52374152H * 0 0 TCTTTACCCTTAGGTCATTTTAGCAACTGTGGAACCAACTGAGTCAATGGATGGAGTAAATAATTCTGTGGTAAATGAGTTTGTCCTTTTGGGTCTCTCTGCTTCTTGGGAGATGAAGATTCTACTcttttttttcttctctgtgttttttgtgGGAATCATGTTTGGAAACctcttcattgtattcactgtgatttttgACCCTCATTTACACTCCCCCATGTATTTCTTGTTGGCCAATCTTTCTCTCATTGACCTGGGTCTGTCTGCTACCACAGTACCAAGGATGATAGTGGACCTTTTCAGTGAATGTAATATAGTCATCTCCTTCCCAGGTTGCATGACACAGATGTTCTTTATCCATGTCATGGGAGGAACTGAGATGGTTCTGCTCATAGTCATGGCATATGACAGATATACAGCAATTTGTAAGCCTCTCCACTATTTGACAATTATGAATCCAAAAATGTGTATTTGCTTTGTAGTGACTGCCTGGATAGTTGGAGTGATCCATGCGATCTCTCAGTTTGTTTTTGTTATAAATTTGCCTTTCTGTGGTCCAAATAAAGTGGAGAGCTTTTATTGTGACTTTCCTCGGGTCATAAAACTTGCGTGCATAGACACCTATAGCCTGGAGTTTGTGGTTATAGCCAATAGTGGTTTTATCTCCATTGGGACTTTTTTCCTATTGATTATCTCCTACATTTTCATCCTGGCCTCTGTTCGACAACATTCTGTCGGTGATTTGTCCAAAGCCTTCTTTACTTTGTCAGCTCACATCACTGTGGTGATTTTATTTTTTGGTCCATGCATGTTTCTTTATGTGTGGCCATTTCCTACATTGTCACTTGATAAATTCTTTGCTATTGTTGACTTTGTTGTCACCCCTGTCTTGAATCCTGCTATCTATACATTAAGGAACAAGGATATGAAGATGGCAATGAGGAGACTGAGCAGCCAGATTGTGAGTTCTAGGGAGAC * NM:i:231 AS:i:2697
+NC_077227.1 0 chr1 69076 2 171835366H2=1X1=1X17=1X12=2X4=1X3=1X1=2X5=2X6=2X3=2X3=1X1=1X3=1X2=1X1=1X2=1X3=1X1=3X4=2X1=2X4=1X2=2X3=1X3=1X4=1X3=1X1=2X1=1X1=2X3=5X9=1X2=1X2=1X1=3I1=1X14=1X2=1X11=1X2=2X4=2X7=1X2=2X1=1X2=1X2=1X1=1X6=1X5=1X1=2X5=1X5=268435455H268435455H52103740H * 0 0 GAGATGAATAACTCTATGGTGAATGAATTCATTTTGTTGGGACTCACCAATTCTTGGGAACTTGAGATTTTCTTTTTtgtggttttctttCTGGCCTATACATTAATCTTGACTGGGAACTTTCTCATTATACTCATGGTGACTCTTGACTCCCATCTGCATTCAACCCCCATGTACTTCCTCCTGGCCAACCTCTCTCTTTTTGACATGTCTCTTTCCACTGTTACTGTCCCCAAAATGATCATAGACTTCTTCAG * NM:i:72 AS:i:601
+NC_077231.1 16 chr1 186299 3 215094373H4=1X1=1X2=1X1=1X1=2I1X1=1X6=1X5=1X23=1X13=2X2=1X1=2X5=1X8=1X2=1X2=1X2=1X2=1X8=1X10=2X2=1X5=1X4=1X3=1X2=1X2=1X2=1X6=1X4=1X1=1X1=1X1=1X2=1X6=1X1=1X1=1X4=1X4=112996753H * 0 0 GCTCTAAGGGCAGGCTTTACCTTGTTcctgttccttctgcttcttcttctcCAGTTTTCGCTCCTTCACACTTCTTAGCTTAGCCTTGCCAATACCTCCTGCCTGGCGGATTGACTCTAGCAAGGTTGCCCGTCCACTGGAAGGATCCACAACTTCCTTGGGCGGTACATGAACTGGAACTAAGaggggggg * NM:i:42 AS:i:612
+NC_077229.1 0 chr1 190587 3 268435455H180369607H2=2X3=3X3=2X3=1X5=1X13=2X3=1X2=1X1=1X2=2X9=2X2=1X4=1X1=3X9=4X3=2X1=2X1=8X5=1X3=1X1=1X3=1X1=1X7=19D2=1X5=1X1=1X1=1X1=2X1=2X2=14I1X6=1X1=3X1=4X1=1X1=1X2=1X2=3X2D1=1X6=1X12=3X2=1X1=1X1=1X1=1X1=2X2=1X2=2X3=1X2=89497099H * 0 0 GATTCCTCATAAAACTCTAGAATGTATTATTAAACAGAAGGTCAGTGAACATCTAGAAAAGGGAGCTGTGAATGAAAGGGGCCAGACTAGCTTCATTTtctttctttttctttttttGACAAGCTTATTAGACTTGCAGAAAAATAGAATTCTTTAGTTATAATTTCAGTCAGAAATTTGAAAAAGCCTCCTGCTACTCTTGTGGACAAGATGGAGACCTGAGAGCTAGCTGATAGGGCATTTA * NM:i:117 AS:i:239
+NC_077228.1 16 chr1 191040 3 268435455H81861412H3=1X3=1X1=3X2=1X6=1X2=1X3=2X5=2X4=2X3=2X2=1X2=1X2=1X2=1X1=2X3=1X5=1X1=1X2=1X1=1X2=2X3=3X1=1X1=1X1=2X3=1X3=1X1=2X1=2X1=1X4=1X1=1X5=1X1=1X1=1X14D4=1X3=10I1X4=1X2=1X2=1X1=1X1=1X1=1X1=1X2=3I3=2X2=2X1=3X1=1X6=2X3=3X1=1X3=1X2=1X4=194390976H * 0 0 TAGGCTGTATCTACAAAGATGCAACTTAATAGGAATGAATGCAAAGTTCAGCACTTGGGGTAAAAATATCAACCTTACACATGAAGAGAATTGGGAAAACATGCCTGGGTGATAGTTTATGTGAAAAGAAGTTAGCTAAAACGGGATGGAAGCACAATATGAGTTCACAGTGACATAATAGACAaaaaaaaaaGCTAATTCAACCTTGGGTTACA * NM:i:100 AS:i:212
+NC_077235.1 0 chr1 194613 1 42909095H3=1X2=2X10=1X7=8I2=2X3=1X2=1X4=3X11=2X5=1X1=1X5=1X12=46505011H * 0 0 TGGTTTCCAATCCTGGCTTTGTCACTTATTCCCAAGATCAGATCACTCAAATTTTCTGTGCCTTTGTTTCTTAATCTAAAAAATGAGATGA * NM:i:24 AS:i:230
+NC_077232.1 0 chr1 200109 2 103349947H3=1X3=1X4=2X3=2X9=1X1=1X4=1I3=2X1=1X2=1X5=1X1=2X3=1X3=2X1=1X5=2X4=207727108H * 0 0 CCGGCCCCACCCAGGCTGCCTGCTCTGCTGGCCCTGCTTGTCTGAGCTCCGGCTCTTGCCCCGGCCCTGCCCACCCC * NM:i:22 AS:i:189
+NC_077227.1 0 chr1 394429 0 24094667H3=1X1=3X3=2X21=1X4=2I2=3X2=1X1=2X1=1X7=1X2=2X3=2X1=1X15=1X4=1X4=1X1=1X2=1X3=2X2=268435455H268435455H199844585H * 0 0 ACCATGCTACTCCAATGTAAACTCCCTGAAAGCAGGGACTATTTTGTTGTCACAGTATCCCCAGTACCTAGCccagtgcctggcACATAGTAGGCACTTACTAAATGCATG * NM:i:29 AS:i:268
+NC_077230.1 0 chr1 403534 0 104187276H10=1X2=1X3=1X3=1I3=1X10=1X6=4X1=1X1=2X1=1X6=2X6=1X4=1X7=1X4=1X14=268435455H82045241H * 0 0 AAAAATCAGAACTGAAGTTACCTTAGACACTACAGTAAAAATGTTGAGATAATATATTGGTCTAATGATTTCTTTTATGAACTCAATTCTAAAATGTTATC * NM:i:20 AS:i:269
221 chr1 160106735 75 + 249250621 SRR359290.9001 0 75 - 75 75
450 chr1 231468663 75 + 249250621 SRR359290.9002 0 75 + 75 75
120 chr15 50775672 24 + 102531392 SRR359290.9002 22 24 + 75 24
=====================================
test/maf-convert-test.sh
=====================================
@@ -51,6 +51,7 @@ maf2=bs100.maf
$r -d sam $maf1
$r -j1e9 sam 90089.maf 102.maf
$r sam toprev.maf
+ $r sam homSap-monDom.maf
head -n999 $maf1 | $r -n tab
head -n999 $maf1 | $r tab
$r -n tab frameshift-new.maf
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/dad6cfa0c2f566403f69c6085a8932a1c259c256
--
View it on GitLab: https://salsa.debian.org/med-team/last-align/-/commit/dad6cfa0c2f566403f69c6085a8932a1c259c256
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20250219/09733776/attachment-0001.htm>
More information about the debian-med-commit
mailing list