Read modification information from modified FASTQ
Source:R/parse_methylation_from_fastq.R
read_modified_fastq.RdThis function reads a modified FASTQ file (e.g. created by samtools fastq -T MM,ML
from a BAM basecalled with a modification-capable model in Dorado or Guppy) to a dataframe.
By default, the dataframe contains columns for unique read id (read), sequence (sequence),
sequence length (sequence_length), quality (quality), comma-separated (via vector_to_string())
modification types present in each read (modification_types), and for each modification type,
a column of comma-separated modification locations (<type>_locations) and
a column of comma-separated modification probabilities (<type>_probabilities).
Modification locations are the indices along the read at which modification was assessed
e.g. a 3 indicates that the third base in the read was assessed for modifications of the given type.
Modification probabilities are the probability that the given modification is present, given as
an integer from 0-255 where integer \(N\) represents the probability space from \(\frac{N}{256}\)
to \(\frac{N+1}{256}\).
To extract the numbers from these columns as numeric vectors to analyse, use string_to_vector() e.g.
list_of_locations <- lapply(test_01$`C+h?_locations`, string_to_vector). Be aware that the SAM
modification types often contain special characters, meaning the colname may need to be enclosed in
backticks as in this example. Alternatively, use extract_methylation_from_dataframe() to
create a list of locations, probabilities, and lengths ready for visualisation in
visualise_methylation(). This works with any modification type extracted in this function,
just provide the relevant colname when calling extract_methylation_from_dataframe().
Optionally (by specifying debug = TRUE), the dataframe will also contain columns of
the raw MM and ML tags (<MM/ML>_raw) and of the same tags with the initial label
trimmed out (<MM/ML>_tags). This is not recommended in most situations but may help
with debugging unexpected issues as it contains the raw data exactly from the FASTQ.
Dataframes produced by this function can be written back to modified FASTQ via write_modified_fastq().
Usage
read_modified_fastq(filename = file.choose(), debug = FALSE)Arguments
- filename
character. The file to be read. Defaults tofile.choose()to select a file interactively.- debug
logical. Boolean value for whether the extra<MM/ML>_tagsand<MM/ML>_rawcolumns should be added to the dataframe. Defaults toFALSEas I can't imagine this is often helpful, but the option is provided to assist with debugging.
Value
dataframe. Dataframe of modification information, as described above.
Sequences can be visualised with visualise_many_sequences() and modification information can be visualised with visualise_methylation() (despite the name, any type of information can be visualised as long as it has locations and probabilities columns).
Can be written back to FASTQ via write_modified_fastq().
Examples
## Locate file
modified_fastq_file <- system.file("extdata",
"example_many_sequences_raw_modified.fastq",
package = "ggDNAvis")
## View file
for (i in 1:16) {
cat(readLines(modified_fastq_file)[i], "\n")
}
#> F1-1a MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0; ML:B:C,26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34,29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41
#> GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> +
#> )8@!9:/0/,0+-6?40,-I601:.';+5,@0.0%)!(20C*,2++*(00#/*+3;E-E)<I5.5G*CB8501;I3'.8233'3><:13)48F?09*>?I90
#> F1-1b MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0; ML:B:C,10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2,10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253
#> GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> +
#> 60-7,7943/*=5=)7<53-I=G6/&/7?8)<$12">/2C;4:9F8:816E,6C3*,1-2139
#> F1-1c MM:Z:C+h?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1; ML:B:C,37,47,64,63,33,64,52,55,17,46,47,64,56,64,56,60,55,58,63,40,45,192,126,129,39,129,183,79,19,195,62,124,173,128,84,159,80,165,141,206
#> TCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> +
#> @9889C8<<*96;52!*86,227.<I.8AI<>;2/391%D19*5@G=8<7<:!7+;:I:-!03<0AI>9?4!57I*-C#25FD24F;
#> F1-1d MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0; ML:B:C,33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55,216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82
#> GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> +
#> :<*1D)89?27#8.3)9<2G<>I.=?58+:.=-8-3%6?7#/FG)198/+3?5/0E1=D9150A4D//650%5.@+@/8>0
## Read file to dataframe
read_modified_fastq(modified_fastq_file, debug = FALSE)
#> read
#> 1 F1-1a
#> 2 F1-1b
#> 3 F1-1c
#> 4 F1-1d
#> 5 F1-1e
#> 6 F1-2a
#> 7 F1-2b
#> 8 F1-3a
#> 9 F1-3b
#> 10 F1-3c
#> 11 F2-1a
#> 12 F2-2a
#> 13 F2-2b
#> 14 F2-2c
#> 15 F3-1a
#> 16 F3-1b
#> 17 F3-2a
#> 18 F3-2b
#> 19 F3-2c
#> 20 F3-3a
#> 21 F3-4a
#> 22 F3-4b
#> 23 F3-4c
#> sequence
#> 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 2 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 3 TCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 4 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 5 TCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCC
#> 6 TCCGCCGCCTCCTCCTCCGCCGCCTCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 7 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA
#> 8 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 9 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGCGGA
#> 10 TCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 11 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA
#> 12 TCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 13 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA
#> 14 TCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 15 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCC
#> 16 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCCGCCGCCGCCGCC
#> 17 GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA
#> 18 GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGA
#> 19 TCCGCCGCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 20 GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA
#> 21 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 22 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGCGGCGGA
#> 23 GGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGA
#> sequence_length
#> 1 102
#> 2 63
#> 3 87
#> 4 81
#> 5 93
#> 6 63
#> 7 69
#> 8 87
#> 9 81
#> 10 84
#> 11 93
#> 12 84
#> 13 87
#> 14 90
#> 15 96
#> 16 96
#> 17 93
#> 18 90
#> 19 87
#> 20 96
#> 21 96
#> 22 81
#> 23 90
#> quality
#> 1 )8@!9:/0/,0+-6?40,-I601:.';+5,@0.0%)!(20C*,2++*(00#/*+3;E-E)<I5.5G*CB8501;I3'.8233'3><:13)48F?09*>?I90
#> 2 60-7,7943/*=5=)7<53-I=G6/&/7?8)<$12">/2C;4:9F8:816E,6C3*,1-2139
#> 3 @9889C8<<*96;52!*86,227.<I.8AI<>;2/391%D19*5@G=8<7<:!7+;:I:-!03<0AI>9?4!57I*-C#25FD24F;
#> 4 :<*1D)89?27#8.3)9<2G<>I.=?58+:.=-8-3%6?7#/FG)198/+3?5/0E1=D9150A4D//650%5.@+@/8>0
#> 5 6<749)6;/@02!.2'40*D79,15),5::=:@-!E7&8?A=D/!#2:.26-57&/I58(C035H>H4,H:%3-;!00!-A6@?84-3E2*4;
#> 6 <-!I79$A.)@@0:5/8>C2,("*(<7-6G4)&.=1CC9I818C(,74:5(<EE/.-")<(6E
#> 7 F='I#*5I:<F?)<4G3&:95*-5?1,!:9BD4B5.-27577<2E9)2:189B.5/*#7;;'**.7;-!
#> 8 ?;.*26<C-8B,3#8/,-9!1++:94:/!A317=9>502=-+8;$=53@D*?/6:6&0D7-.@8,5;F,1?0D?$9'&665B8.604
#> 9 *46.5//3:37?24:(:0*#.))E)?:,/172=2!4">.*/;"8+5<;D6.I2=>:C3)108,<)GC161)!55E!.>86/
#> 10 1;3*=4G5'+()0A659+2;3/!;34:%0E432(38@3+I?924C4E-4;*4&*9-6A64>66G5',I2<962C121B@A/637
#> 11 =</-I354/,*>+<CA40*537/;<@I7/4%6192'5'>#4:&C,072+90:0+4;74"D5,38&<7A?00+1>G>#=?;,@<<1=64D=!1&
#> 12 7;86<>H.)-1H+7I6.+39!4>5=!F483+;5=-7.4!*821*6$I'DI):=+0?3-(<7;.791062#H2.1<*7145:>1;
#> 13 7?38,EC#3::=1)8&;<">3.9BE)1661!2)5-4.11B<3)?')-+,B4.<7)/:IE=5$.3:66G9216-C20,>(0848(1$-
#> 14 2>%AC6.?G=59+1=+EC?264?'B6$1@<7D99->$18+*;1!@?8>9645+23B/<=*.6/6543BI494E84)1=9;/8=6+/,68@
#> 15 7);7-=464F1;7;(83B84.@79.>,!>?>16;,6:=/@B;C:;63+/+;69;?@&>I'01!-3H%.,6;=-3=!A5'.-)9@?8*?346C<2*/
#> 16 :C8E6789(=9%1.66A463B5/B8;A51=?=<,8/461!058!6354!<609I9@:7.E.38)7;@@6/C?D&,*%D,I6>6:4%9(1/7>$<C/
#> 17 :0I4099<,4E01;/@96%2I2<,%<C&=81F+4<*@4A5.('4!%I3CE657<=!5;37>4D:%3;7'"4<.9;?;7%0>:,84B512,B7/
#> 18 9>124!752+@06I/.72097*';-+A60=B?+/8'15477>4-435D;G@G'./21:(0/1/A=7'I>A"3=9;;12,@"2=3D=,458
#> 19 <<95G42/@E!1)A68,'%=60C4)3,;9C/;A8<6!-(?83,,194*49G1-,:64E-?/!/,*07AA!G?-9=!(/-+6/@>2/0
#> 20 $<,5"7+!$';8<0794*@FI>34224!57+#1!F<+53$,?)-.A3;=1*71C02<.5:1)82!86$03/;%+1C3+D3;@9B-E#+/70;9<D'
#> 21 53?I.;)/.91%3:6)0041C)I;2<"3:8?*954::080?3<?>=7A;/#5D?;I2@075;:C.-4HI3GE+-?.,I>)I!>4(5(:1"2-#-2?
#> 22 .85$#;!1F$8E:B+;7CI6@11/'65<3,4G:8@GF1413:0)3CH1=44.%G=#2E67=?;9DF7358.;(I!74:1I4
#> 23 5@<733';9+3BB)=69,3!.2B*86'8E>@3?!(36:<002/4>:1.43A!+;<.3G*G8?0*991,B(C/"I9*1-86)8.;;5-0+=
#> modification_types
#> 1 C+h?,C+m?
#> 2 C+h?,C+m?
#> 3 C+h?,C+m?
#> 4 C+h?,C+m?
#> 5 C+h?,C+m?
#> 6 C+h?,C+m?
#> 7 C+h?,C+m?
#> 8 C+h?,C+m?
#> 9 C+h?,C+m?
#> 10 C+h?,C+m?
#> 11 C+h?,C+m?
#> 12 C+h?,C+m?
#> 13 C+h?,C+m?
#> 14 C+h?,C+m?
#> 15 C+h?,C+m?
#> 16 C+h?,C+m?
#> 17 C+h?,C+m?
#> 18 C+h?,C+m?
#> 19 C+h?,C+m?
#> 20 C+h?,C+m?
#> 21 C+h?,C+m?
#> 22 C+h?,C+m?
#> 23 C+h?,C+m?
#> C+h?_locations
#> 1 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99
#> 2 3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60
#> 3 3,6,15,18,21,30,33,36,45,48,51,60,63,66,69,72,75,78,81,84
#> 4 3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78
#> 5 3,6,15,18,21,30,33,36,45,48,51,60,63,66,75,78,81,84,87,90
#> 6 3,6,18,21,33,36,39,42,45,48,51,54,57,60
#> 7 3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66
#> 8 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84
#> 9 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78
#> 10 3,6,15,18,27,30,33,42,45,48,57,60,63,66,69,72,75,78,81
#> 11 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90
#> 12 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81
#> 13 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84
#> 14 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81,84,87
#> 15 3,6,15,18,27,30,39,42,51,54,63,66,75,78,87,90,93
#> 16 3,6,15,18,27,30,39,42,51,54,63,66,75,78,81,84,87,90,93
#> 17 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90
#> 18 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87
#> 19 3,6,9,12,21,24,33,36,45,48,57,60,63,66,69,72,75,78,81,84
#> 20 3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93
#> 21 3,6,15,18,27,30,39,42,51,54,63,66,69,72,75,78,81,84,87,90,93
#> 22 3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78
#> 23 3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87
#> C+h?_probabilities
#> 1 26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34
#> 2 10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2
#> 3 37,47,64,63,33,64,52,55,17,46,47,64,56,64,56,60,55,58,63,40
#> 4 33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55
#> 5 54,7,53,64,24,29,30,23,35,23,34,55,61,23,40,63,31,64,18,57
#> 6 12,23,52,9,63,29,33,56,30,41,52,63,9,49
#> 7 27,44,20,13,51,28,41,48,19,1,14,64,52,48,64,64
#> 8 55,10,59,28,62,20,64,21,62,59,29,64,4,56,64,59,60,49,63,5
#> 9 62,63,45,19,32,46,3,61,0,159,42,80,46,84,86,52,8,92,102,4,138,20
#> 10 20,111,79,1,238,1,142,35,80,40,21,126,47,112,21,71,103,43,80
#> 11 68,1,220,4,42,36,35,57,3,90,56,79,92,19,93,36,130,47,82,1,109,104,58,11,83,10,86,49
#> 12 49,82,145,1,40,133,14,114,89,5,129,88,26,66,42,136,25,17,74,44,6,104,125,18,93
#> 13 17,3,130,28,84,5,50,95,55,112,49,67,7,106,67,0,72,21,209,3,112,60,28,6,188,4
#> 14 38,24,184,5,98,72,32,22,83,39,135,53,51,9,54,55,45,102,95,23,3,198,19,121,22,123,3
#> 15 103,74,17,32,114,0,93,133,6,77,116,2,51,112,11,157,59
#> 16 22,63,13,16,88,54,55,26,86,133,7,170,15,68,29,41,30,89,61
#> 17 11,195,26,74,62,93,1,139,5,178,33,3,158,65,76,3,13,225
#> 18 9,13,165,10,0,10,104,65,78,43,124,87,0,95,19,2,73
#> 19 17,24,0,47,75,133,76,9,112,90,19,75,156,35,30,136,5,16,30,191
#> 20 24,3,3,78,63,47,66,155,13,19,109,141,87,2,55,43,24,83,161
#> 21 225,21,6,207,111,10,11,116,113,24,108,32,33,162,6,20,35,14,73,44,36
#> 22 29,9,79,29,15,95,14,82,81,43,11,25,98,35,18,53,112,2,57,31
#> 23 52,87,155,117,2,0,3,50,81,184,75,74,60,97,15,8,46,188,81
#> C+m?_locations
#> 1 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99
#> 2 3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60
#> 3 3,6,15,18,21,30,33,36,45,48,51,60,63,66,69,72,75,78,81,84
#> 4 3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78
#> 5 3,6,15,18,21,30,33,36,45,48,51,60,63,66,75,78,81,84,87,90
#> 6 3,6,18,21,33,36,39,42,45,48,51,54,57,60
#> 7 3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66
#> 8 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84
#> 9 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78
#> 10 3,6,15,18,27,30,33,42,45,48,57,60,63,66,69,72,75,78,81
#> 11 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90
#> 12 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81
#> 13 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84
#> 14 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81,84,87
#> 15 3,6,15,18,27,30,39,42,51,54,63,66,75,78,87,90,93
#> 16 3,6,15,18,27,30,39,42,51,54,63,66,75,78,81,84,87,90,93
#> 17 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90
#> 18 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87
#> 19 3,6,9,12,21,24,33,36,45,48,57,60,63,66,69,72,75,78,81,84
#> 20 3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93
#> 21 3,6,15,18,27,30,39,42,51,54,63,66,69,72,75,78,81,84,87,90,93
#> 22 3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78
#> 23 3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87
#> C+m?_probabilities
#> 1 29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41
#> 2 10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253
#> 3 45,192,126,129,39,129,183,79,19,195,62,124,173,128,84,159,80,165,141,206
#> 4 216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82
#> 5 79,7,77,130,27,34,34,230,42,229,41,79,99,229,50,139,36,120,236,170
#> 6 242,26,182,10,111,33,40,83,34,52,71,144,9,189
#> 7 31,56,233,241,71,31,203,190,234,254,240,124,72,64,128,127
#> 8 81,245,162,32,108,233,119,232,152,161,222,128,251,83,123,91,160,189,144,250
#> 9 147,112,58,21,217,60,252,153,255,96,142,110,147,110,57,22,163,110,19,205,83,193
#> 10 189,79,161,215,6,244,19,153,88,122,77,30,143,108,194,88,109,181,149
#> 11 163,253,33,225,207,210,213,187,251,163,168,135,81,196,134,187,78,103,52,251,144,71,47,193,145,238,163,179
#> 12 55,62,108,252,125,78,191,54,145,206,27,145,203,126,130,86,205,127,34,85,66,8,108,217,122
#> 13 176,250,122,197,146,246,203,136,152,67,71,17,144,67,1,150,133,215,8,153,68,31,26,191,4,13
#> 14 193,155,62,243,105,167,209,178,73,116,72,188,200,234,109,94,88,68,139,209,129,7,204,96,194,91,191
#> 15 104,174,233,196,140,253,49,115,242,113,137,250,90,79,162,29,177
#> 16 225,187,235,168,48,109,94,87,39,101,220,51,213,89,104,49,50,37,104
#> 17 243,50,121,98,95,7,237,105,244,69,132,249,94,79,9,170,235,11
#> 18 51,190,33,181,255,241,151,186,124,196,1,142,117,84,213,249,168
#> 19 175,29,55,27,1,53,75,168,107,26,194,101,78,124,224,68,249,185,209,60
#> 20 49,251,241,176,189,187,166,43,235,144,137,5,93,175,106,193,198,146,48
#> 21 14,51,238,27,88,231,169,105,34,198,131,106,221,55,247,206,198,106,159,24,193
#> 22 109,86,70,169,200,112,237,69,168,97,239,188,150,208,225,190,128,252,142,224
#> 23 161,156,9,65,198,255,245,191,174,63,155,146,13,95,228,100,132,45,49
read_modified_fastq(modified_fastq_file, debug = TRUE)
#> read
#> 1 F1-1a
#> 2 F1-1b
#> 3 F1-1c
#> 4 F1-1d
#> 5 F1-1e
#> 6 F1-2a
#> 7 F1-2b
#> 8 F1-3a
#> 9 F1-3b
#> 10 F1-3c
#> 11 F2-1a
#> 12 F2-2a
#> 13 F2-2b
#> 14 F2-2c
#> 15 F3-1a
#> 16 F3-1b
#> 17 F3-2a
#> 18 F3-2b
#> 19 F3-2c
#> 20 F3-3a
#> 21 F3-4a
#> 22 F3-4b
#> 23 F3-4c
#> sequence
#> 1 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 2 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 3 TCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 4 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 5 TCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCC
#> 6 TCCGCCGCCTCCTCCTCCGCCGCCTCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 7 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGAGGCGGCGGAGGAGGAGGCGGCGGA
#> 8 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGA
#> 9 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGCGGAGGAGGCGGCGGCGGCGGA
#> 10 TCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 11 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA
#> 12 TCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 13 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGA
#> 14 TCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 15 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCC
#> 16 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCCGCCGCCGCCGCC
#> 17 GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA
#> 18 GGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGA
#> 19 TCCGCCGCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCTCCTCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 20 GGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGA
#> 21 TCCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCACCACCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC
#> 22 GGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGTGGTGGCGGCGGCGGCGGA
#> 23 GGCGGCGGCGGCGGCGGCGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGAGGAGGCGGCGGCGGA
#> sequence_length
#> 1 102
#> 2 63
#> 3 87
#> 4 81
#> 5 93
#> 6 63
#> 7 69
#> 8 87
#> 9 81
#> 10 84
#> 11 93
#> 12 84
#> 13 87
#> 14 90
#> 15 96
#> 16 96
#> 17 93
#> 18 90
#> 19 87
#> 20 96
#> 21 96
#> 22 81
#> 23 90
#> quality
#> 1 )8@!9:/0/,0+-6?40,-I601:.';+5,@0.0%)!(20C*,2++*(00#/*+3;E-E)<I5.5G*CB8501;I3'.8233'3><:13)48F?09*>?I90
#> 2 60-7,7943/*=5=)7<53-I=G6/&/7?8)<$12">/2C;4:9F8:816E,6C3*,1-2139
#> 3 @9889C8<<*96;52!*86,227.<I.8AI<>;2/391%D19*5@G=8<7<:!7+;:I:-!03<0AI>9?4!57I*-C#25FD24F;
#> 4 :<*1D)89?27#8.3)9<2G<>I.=?58+:.=-8-3%6?7#/FG)198/+3?5/0E1=D9150A4D//650%5.@+@/8>0
#> 5 6<749)6;/@02!.2'40*D79,15),5::=:@-!E7&8?A=D/!#2:.26-57&/I58(C035H>H4,H:%3-;!00!-A6@?84-3E2*4;
#> 6 <-!I79$A.)@@0:5/8>C2,("*(<7-6G4)&.=1CC9I818C(,74:5(<EE/.-")<(6E
#> 7 F='I#*5I:<F?)<4G3&:95*-5?1,!:9BD4B5.-27577<2E9)2:189B.5/*#7;;'**.7;-!
#> 8 ?;.*26<C-8B,3#8/,-9!1++:94:/!A317=9>502=-+8;$=53@D*?/6:6&0D7-.@8,5;F,1?0D?$9'&665B8.604
#> 9 *46.5//3:37?24:(:0*#.))E)?:,/172=2!4">.*/;"8+5<;D6.I2=>:C3)108,<)GC161)!55E!.>86/
#> 10 1;3*=4G5'+()0A659+2;3/!;34:%0E432(38@3+I?924C4E-4;*4&*9-6A64>66G5',I2<962C121B@A/637
#> 11 =</-I354/,*>+<CA40*537/;<@I7/4%6192'5'>#4:&C,072+90:0+4;74"D5,38&<7A?00+1>G>#=?;,@<<1=64D=!1&
#> 12 7;86<>H.)-1H+7I6.+39!4>5=!F483+;5=-7.4!*821*6$I'DI):=+0?3-(<7;.791062#H2.1<*7145:>1;
#> 13 7?38,EC#3::=1)8&;<">3.9BE)1661!2)5-4.11B<3)?')-+,B4.<7)/:IE=5$.3:66G9216-C20,>(0848(1$-
#> 14 2>%AC6.?G=59+1=+EC?264?'B6$1@<7D99->$18+*;1!@?8>9645+23B/<=*.6/6543BI494E84)1=9;/8=6+/,68@
#> 15 7);7-=464F1;7;(83B84.@79.>,!>?>16;,6:=/@B;C:;63+/+;69;?@&>I'01!-3H%.,6;=-3=!A5'.-)9@?8*?346C<2*/
#> 16 :C8E6789(=9%1.66A463B5/B8;A51=?=<,8/461!058!6354!<609I9@:7.E.38)7;@@6/C?D&,*%D,I6>6:4%9(1/7>$<C/
#> 17 :0I4099<,4E01;/@96%2I2<,%<C&=81F+4<*@4A5.('4!%I3CE657<=!5;37>4D:%3;7'"4<.9;?;7%0>:,84B512,B7/
#> 18 9>124!752+@06I/.72097*';-+A60=B?+/8'15477>4-435D;G@G'./21:(0/1/A=7'I>A"3=9;;12,@"2=3D=,458
#> 19 <<95G42/@E!1)A68,'%=60C4)3,;9C/;A8<6!-(?83,,194*49G1-,:64E-?/!/,*07AA!G?-9=!(/-+6/@>2/0
#> 20 $<,5"7+!$';8<0794*@FI>34224!57+#1!F<+53$,?)-.A3;=1*71C02<.5:1)82!86$03/;%+1C3+D3;@9B-E#+/70;9<D'
#> 21 53?I.;)/.91%3:6)0041C)I;2<"3:8?*954::080?3<?>=7A;/#5D?;I2@075;:C.-4HI3GE+-?.,I>)I!>4(5(:1"2-#-2?
#> 22 .85$#;!1F$8E:B+;7CI6@11/'65<3,4G:8@GF1413:0)3CH1=44.%G=#2E67=?;9DF7358.;(I!74:1I4
#> 23 5@<733';9+3BB)=69,3!.2B*86'8E>@3?!(36:<002/4>:1.43A!+;<.3G*G8?0*991,B(C/"I9*1-86)8.;;5-0+=
#> modification_types
#> 1 C+h?,C+m?
#> 2 C+h?,C+m?
#> 3 C+h?,C+m?
#> 4 C+h?,C+m?
#> 5 C+h?,C+m?
#> 6 C+h?,C+m?
#> 7 C+h?,C+m?
#> 8 C+h?,C+m?
#> 9 C+h?,C+m?
#> 10 C+h?,C+m?
#> 11 C+h?,C+m?
#> 12 C+h?,C+m?
#> 13 C+h?,C+m?
#> 14 C+h?,C+m?
#> 15 C+h?,C+m?
#> 16 C+h?,C+m?
#> 17 C+h?,C+m?
#> 18 C+h?,C+m?
#> 19 C+h?,C+m?
#> 20 C+h?,C+m?
#> 21 C+h?,C+m?
#> 22 C+h?,C+m?
#> 23 C+h?,C+m?
#> MM_tags
#> 1 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 2 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 3 C+h?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;
#> 4 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 5 C+h?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1;C+m?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1;
#> 6 C+h?,1,1,7,1,7,1,1,1,1,1,1,1,1,1;C+m?,1,1,7,1,7,1,1,1,1,1,1,1,1,1;
#> 7 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 8 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 9 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 10 C+h?,1,1,5,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;
#> 11 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 12 C+h?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;
#> 13 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 14 C+h?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;
#> 15 C+h?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,5,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,5,1,1;
#> 16 C+h?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1;
#> 17 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 18 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 19 C+h?,1,1,1,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1;C+m?,1,1,1,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1;
#> 20 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 21 C+h?,1,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1,1;
#> 22 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 23 C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> ML_tags
#> 1 26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34,29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41
#> 2 10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2,10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253
#> 3 37,47,64,63,33,64,52,55,17,46,47,64,56,64,56,60,55,58,63,40,45,192,126,129,39,129,183,79,19,195,62,124,173,128,84,159,80,165,141,206
#> 4 33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55,216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82
#> 5 54,7,53,64,24,29,30,23,35,23,34,55,61,23,40,63,31,64,18,57,79,7,77,130,27,34,34,230,42,229,41,79,99,229,50,139,36,120,236,170
#> 6 12,23,52,9,63,29,33,56,30,41,52,63,9,49,242,26,182,10,111,33,40,83,34,52,71,144,9,189
#> 7 27,44,20,13,51,28,41,48,19,1,14,64,52,48,64,64,31,56,233,241,71,31,203,190,234,254,240,124,72,64,128,127
#> 8 55,10,59,28,62,20,64,21,62,59,29,64,4,56,64,59,60,49,63,5,81,245,162,32,108,233,119,232,152,161,222,128,251,83,123,91,160,189,144,250
#> 9 62,63,45,19,32,46,3,61,0,159,42,80,46,84,86,52,8,92,102,4,138,20,147,112,58,21,217,60,252,153,255,96,142,110,147,110,57,22,163,110,19,205,83,193
#> 10 20,111,79,1,238,1,142,35,80,40,21,126,47,112,21,71,103,43,80,189,79,161,215,6,244,19,153,88,122,77,30,143,108,194,88,109,181,149
#> 11 68,1,220,4,42,36,35,57,3,90,56,79,92,19,93,36,130,47,82,1,109,104,58,11,83,10,86,49,163,253,33,225,207,210,213,187,251,163,168,135,81,196,134,187,78,103,52,251,144,71,47,193,145,238,163,179
#> 12 49,82,145,1,40,133,14,114,89,5,129,88,26,66,42,136,25,17,74,44,6,104,125,18,93,55,62,108,252,125,78,191,54,145,206,27,145,203,126,130,86,205,127,34,85,66,8,108,217,122
#> 13 17,3,130,28,84,5,50,95,55,112,49,67,7,106,67,0,72,21,209,3,112,60,28,6,188,4,176,250,122,197,146,246,203,136,152,67,71,17,144,67,1,150,133,215,8,153,68,31,26,191,4,13
#> 14 38,24,184,5,98,72,32,22,83,39,135,53,51,9,54,55,45,102,95,23,3,198,19,121,22,123,3,193,155,62,243,105,167,209,178,73,116,72,188,200,234,109,94,88,68,139,209,129,7,204,96,194,91,191
#> 15 103,74,17,32,114,0,93,133,6,77,116,2,51,112,11,157,59,104,174,233,196,140,253,49,115,242,113,137,250,90,79,162,29,177
#> 16 22,63,13,16,88,54,55,26,86,133,7,170,15,68,29,41,30,89,61,225,187,235,168,48,109,94,87,39,101,220,51,213,89,104,49,50,37,104
#> 17 11,195,26,74,62,93,1,139,5,178,33,3,158,65,76,3,13,225,243,50,121,98,95,7,237,105,244,69,132,249,94,79,9,170,235,11
#> 18 9,13,165,10,0,10,104,65,78,43,124,87,0,95,19,2,73,51,190,33,181,255,241,151,186,124,196,1,142,117,84,213,249,168
#> 19 17,24,0,47,75,133,76,9,112,90,19,75,156,35,30,136,5,16,30,191,175,29,55,27,1,53,75,168,107,26,194,101,78,124,224,68,249,185,209,60
#> 20 24,3,3,78,63,47,66,155,13,19,109,141,87,2,55,43,24,83,161,49,251,241,176,189,187,166,43,235,144,137,5,93,175,106,193,198,146,48
#> 21 225,21,6,207,111,10,11,116,113,24,108,32,33,162,6,20,35,14,73,44,36,14,51,238,27,88,231,169,105,34,198,131,106,221,55,247,206,198,106,159,24,193
#> 22 29,9,79,29,15,95,14,82,81,43,11,25,98,35,18,53,112,2,57,31,109,86,70,169,200,112,237,69,168,97,239,188,150,208,225,190,128,252,142,224
#> 23 52,87,155,117,2,0,3,50,81,184,75,74,60,97,15,8,46,188,81,161,156,9,65,198,255,245,191,174,63,155,146,13,95,228,100,132,45,49
#> MM_raw
#> 1 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 2 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 3 MM:Z:C+h?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;
#> 4 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 5 MM:Z:C+h?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1;C+m?,1,1,5,1,1,5,1,1,5,1,1,5,1,1,5,1,1,1,1,1;
#> 6 MM:Z:C+h?,1,1,7,1,7,1,1,1,1,1,1,1,1,1;C+m?,1,1,7,1,7,1,1,1,1,1,1,1,1,1;
#> 7 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 8 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 9 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 10 MM:Z:C+h?,1,1,5,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,1,5,1,1,5,1,1,1,1,1,1,1,1;
#> 11 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 12 MM:Z:C+h?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;
#> 13 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 14 MM:Z:C+h?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1;
#> 15 MM:Z:C+h?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,5,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,5,1,1;
#> 16 MM:Z:C+h?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1;
#> 17 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 18 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 19 MM:Z:C+h?,1,1,1,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1;C+m?,1,1,1,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1;
#> 20 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 21 MM:Z:C+h?,1,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1,1;C+m?,1,1,5,1,5,1,5,1,5,1,5,1,1,1,1,1,1,1,1,1,1;
#> 22 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> 23 MM:Z:C+h?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;C+m?,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;
#> ML_raw
#> 1 ML:B:C,26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34,29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41
#> 2 ML:B:C,10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2,10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253
#> 3 ML:B:C,37,47,64,63,33,64,52,55,17,46,47,64,56,64,56,60,55,58,63,40,45,192,126,129,39,129,183,79,19,195,62,124,173,128,84,159,80,165,141,206
#> 4 ML:B:C,33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55,216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82
#> 5 ML:B:C,54,7,53,64,24,29,30,23,35,23,34,55,61,23,40,63,31,64,18,57,79,7,77,130,27,34,34,230,42,229,41,79,99,229,50,139,36,120,236,170
#> 6 ML:B:C,12,23,52,9,63,29,33,56,30,41,52,63,9,49,242,26,182,10,111,33,40,83,34,52,71,144,9,189
#> 7 ML:B:C,27,44,20,13,51,28,41,48,19,1,14,64,52,48,64,64,31,56,233,241,71,31,203,190,234,254,240,124,72,64,128,127
#> 8 ML:B:C,55,10,59,28,62,20,64,21,62,59,29,64,4,56,64,59,60,49,63,5,81,245,162,32,108,233,119,232,152,161,222,128,251,83,123,91,160,189,144,250
#> 9 ML:B:C,62,63,45,19,32,46,3,61,0,159,42,80,46,84,86,52,8,92,102,4,138,20,147,112,58,21,217,60,252,153,255,96,142,110,147,110,57,22,163,110,19,205,83,193
#> 10 ML:B:C,20,111,79,1,238,1,142,35,80,40,21,126,47,112,21,71,103,43,80,189,79,161,215,6,244,19,153,88,122,77,30,143,108,194,88,109,181,149
#> 11 ML:B:C,68,1,220,4,42,36,35,57,3,90,56,79,92,19,93,36,130,47,82,1,109,104,58,11,83,10,86,49,163,253,33,225,207,210,213,187,251,163,168,135,81,196,134,187,78,103,52,251,144,71,47,193,145,238,163,179
#> 12 ML:B:C,49,82,145,1,40,133,14,114,89,5,129,88,26,66,42,136,25,17,74,44,6,104,125,18,93,55,62,108,252,125,78,191,54,145,206,27,145,203,126,130,86,205,127,34,85,66,8,108,217,122
#> 13 ML:B:C,17,3,130,28,84,5,50,95,55,112,49,67,7,106,67,0,72,21,209,3,112,60,28,6,188,4,176,250,122,197,146,246,203,136,152,67,71,17,144,67,1,150,133,215,8,153,68,31,26,191,4,13
#> 14 ML:B:C,38,24,184,5,98,72,32,22,83,39,135,53,51,9,54,55,45,102,95,23,3,198,19,121,22,123,3,193,155,62,243,105,167,209,178,73,116,72,188,200,234,109,94,88,68,139,209,129,7,204,96,194,91,191
#> 15 ML:B:C,103,74,17,32,114,0,93,133,6,77,116,2,51,112,11,157,59,104,174,233,196,140,253,49,115,242,113,137,250,90,79,162,29,177
#> 16 ML:B:C,22,63,13,16,88,54,55,26,86,133,7,170,15,68,29,41,30,89,61,225,187,235,168,48,109,94,87,39,101,220,51,213,89,104,49,50,37,104
#> 17 ML:B:C,11,195,26,74,62,93,1,139,5,178,33,3,158,65,76,3,13,225,243,50,121,98,95,7,237,105,244,69,132,249,94,79,9,170,235,11
#> 18 ML:B:C,9,13,165,10,0,10,104,65,78,43,124,87,0,95,19,2,73,51,190,33,181,255,241,151,186,124,196,1,142,117,84,213,249,168
#> 19 ML:B:C,17,24,0,47,75,133,76,9,112,90,19,75,156,35,30,136,5,16,30,191,175,29,55,27,1,53,75,168,107,26,194,101,78,124,224,68,249,185,209,60
#> 20 ML:B:C,24,3,3,78,63,47,66,155,13,19,109,141,87,2,55,43,24,83,161,49,251,241,176,189,187,166,43,235,144,137,5,93,175,106,193,198,146,48
#> 21 ML:B:C,225,21,6,207,111,10,11,116,113,24,108,32,33,162,6,20,35,14,73,44,36,14,51,238,27,88,231,169,105,34,198,131,106,221,55,247,206,198,106,159,24,193
#> 22 ML:B:C,29,9,79,29,15,95,14,82,81,43,11,25,98,35,18,53,112,2,57,31,109,86,70,169,200,112,237,69,168,97,239,188,150,208,225,190,128,252,142,224
#> 23 ML:B:C,52,87,155,117,2,0,3,50,81,184,75,74,60,97,15,8,46,188,81,161,156,9,65,198,255,245,191,174,63,155,146,13,95,228,100,132,45,49
#> C+h?_locations
#> 1 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99
#> 2 3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60
#> 3 3,6,15,18,21,30,33,36,45,48,51,60,63,66,69,72,75,78,81,84
#> 4 3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78
#> 5 3,6,15,18,21,30,33,36,45,48,51,60,63,66,75,78,81,84,87,90
#> 6 3,6,18,21,33,36,39,42,45,48,51,54,57,60
#> 7 3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66
#> 8 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84
#> 9 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78
#> 10 3,6,15,18,27,30,33,42,45,48,57,60,63,66,69,72,75,78,81
#> 11 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90
#> 12 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81
#> 13 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84
#> 14 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81,84,87
#> 15 3,6,15,18,27,30,39,42,51,54,63,66,75,78,87,90,93
#> 16 3,6,15,18,27,30,39,42,51,54,63,66,75,78,81,84,87,90,93
#> 17 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90
#> 18 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87
#> 19 3,6,9,12,21,24,33,36,45,48,57,60,63,66,69,72,75,78,81,84
#> 20 3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93
#> 21 3,6,15,18,27,30,39,42,51,54,63,66,69,72,75,78,81,84,87,90,93
#> 22 3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78
#> 23 3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87
#> C+h?_probabilities
#> 1 26,60,61,60,30,59,2,46,57,64,54,63,52,18,53,34,52,50,39,46,55,54,34
#> 2 10,44,39,64,20,36,11,63,50,54,64,38,46,41,49,2
#> 3 37,47,64,63,33,64,52,55,17,46,47,64,56,64,56,60,55,58,63,40
#> 4 33,29,10,55,3,46,53,54,64,12,63,27,24,4,43,21,64,60,17,55
#> 5 54,7,53,64,24,29,30,23,35,23,34,55,61,23,40,63,31,64,18,57
#> 6 12,23,52,9,63,29,33,56,30,41,52,63,9,49
#> 7 27,44,20,13,51,28,41,48,19,1,14,64,52,48,64,64
#> 8 55,10,59,28,62,20,64,21,62,59,29,64,4,56,64,59,60,49,63,5
#> 9 62,63,45,19,32,46,3,61,0,159,42,80,46,84,86,52,8,92,102,4,138,20
#> 10 20,111,79,1,238,1,142,35,80,40,21,126,47,112,21,71,103,43,80
#> 11 68,1,220,4,42,36,35,57,3,90,56,79,92,19,93,36,130,47,82,1,109,104,58,11,83,10,86,49
#> 12 49,82,145,1,40,133,14,114,89,5,129,88,26,66,42,136,25,17,74,44,6,104,125,18,93
#> 13 17,3,130,28,84,5,50,95,55,112,49,67,7,106,67,0,72,21,209,3,112,60,28,6,188,4
#> 14 38,24,184,5,98,72,32,22,83,39,135,53,51,9,54,55,45,102,95,23,3,198,19,121,22,123,3
#> 15 103,74,17,32,114,0,93,133,6,77,116,2,51,112,11,157,59
#> 16 22,63,13,16,88,54,55,26,86,133,7,170,15,68,29,41,30,89,61
#> 17 11,195,26,74,62,93,1,139,5,178,33,3,158,65,76,3,13,225
#> 18 9,13,165,10,0,10,104,65,78,43,124,87,0,95,19,2,73
#> 19 17,24,0,47,75,133,76,9,112,90,19,75,156,35,30,136,5,16,30,191
#> 20 24,3,3,78,63,47,66,155,13,19,109,141,87,2,55,43,24,83,161
#> 21 225,21,6,207,111,10,11,116,113,24,108,32,33,162,6,20,35,14,73,44,36
#> 22 29,9,79,29,15,95,14,82,81,43,11,25,98,35,18,53,112,2,57,31
#> 23 52,87,155,117,2,0,3,50,81,184,75,74,60,97,15,8,46,188,81
#> C+m?_locations
#> 1 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84,87,96,99
#> 2 3,6,9,12,15,18,21,24,27,30,33,42,45,48,57,60
#> 3 3,6,15,18,21,30,33,36,45,48,51,60,63,66,69,72,75,78,81,84
#> 4 3,6,9,12,15,18,21,24,27,30,33,36,45,48,51,60,63,66,75,78
#> 5 3,6,15,18,21,30,33,36,45,48,51,60,63,66,75,78,81,84,87,90
#> 6 3,6,18,21,33,36,39,42,45,48,51,54,57,60
#> 7 3,6,9,12,15,18,21,24,27,30,33,36,48,51,63,66
#> 8 3,6,9,12,15,18,21,24,27,36,39,42,51,54,57,66,69,72,81,84
#> 9 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,54,57,60,69,72,75,78
#> 10 3,6,15,18,27,30,33,42,45,48,57,60,63,66,69,72,75,78,81
#> 11 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,87,90
#> 12 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81
#> 13 3,6,9,12,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,81,84
#> 14 3,6,15,18,21,24,27,30,33,36,39,42,45,48,51,54,57,60,63,66,69,72,75,78,81,84,87
#> 15 3,6,15,18,27,30,39,42,51,54,63,66,75,78,87,90,93
#> 16 3,6,15,18,27,30,39,42,51,54,63,66,75,78,81,84,87,90,93
#> 17 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87,90
#> 18 3,6,9,12,15,18,27,30,39,42,51,54,63,66,75,78,87
#> 19 3,6,9,12,21,24,33,36,45,48,57,60,63,66,69,72,75,78,81,84
#> 20 3,6,9,12,15,18,21,30,33,42,45,54,57,66,69,78,81,90,93
#> 21 3,6,15,18,27,30,39,42,51,54,63,66,69,72,75,78,81,84,87,90,93
#> 22 3,6,9,12,15,18,21,24,27,30,33,36,45,48,57,60,69,72,75,78
#> 23 3,6,9,12,15,18,21,24,33,36,45,48,57,60,69,72,81,84,87
#> C+m?_probabilities
#> 1 29,159,155,159,220,163,2,59,170,131,177,139,72,235,75,214,73,68,48,59,81,77,41
#> 2 10,56,207,134,233,212,12,116,68,78,129,46,194,51,66,253
#> 3 45,192,126,129,39,129,183,79,19,195,62,124,173,128,84,159,80,165,141,206
#> 4 216,221,11,81,4,61,180,79,130,13,144,31,228,4,200,23,132,98,18,82
#> 5 79,7,77,130,27,34,34,230,42,229,41,79,99,229,50,139,36,120,236,170
#> 6 242,26,182,10,111,33,40,83,34,52,71,144,9,189
#> 7 31,56,233,241,71,31,203,190,234,254,240,124,72,64,128,127
#> 8 81,245,162,32,108,233,119,232,152,161,222,128,251,83,123,91,160,189,144,250
#> 9 147,112,58,21,217,60,252,153,255,96,142,110,147,110,57,22,163,110,19,205,83,193
#> 10 189,79,161,215,6,244,19,153,88,122,77,30,143,108,194,88,109,181,149
#> 11 163,253,33,225,207,210,213,187,251,163,168,135,81,196,134,187,78,103,52,251,144,71,47,193,145,238,163,179
#> 12 55,62,108,252,125,78,191,54,145,206,27,145,203,126,130,86,205,127,34,85,66,8,108,217,122
#> 13 176,250,122,197,146,246,203,136,152,67,71,17,144,67,1,150,133,215,8,153,68,31,26,191,4,13
#> 14 193,155,62,243,105,167,209,178,73,116,72,188,200,234,109,94,88,68,139,209,129,7,204,96,194,91,191
#> 15 104,174,233,196,140,253,49,115,242,113,137,250,90,79,162,29,177
#> 16 225,187,235,168,48,109,94,87,39,101,220,51,213,89,104,49,50,37,104
#> 17 243,50,121,98,95,7,237,105,244,69,132,249,94,79,9,170,235,11
#> 18 51,190,33,181,255,241,151,186,124,196,1,142,117,84,213,249,168
#> 19 175,29,55,27,1,53,75,168,107,26,194,101,78,124,224,68,249,185,209,60
#> 20 49,251,241,176,189,187,166,43,235,144,137,5,93,175,106,193,198,146,48
#> 21 14,51,238,27,88,231,169,105,34,198,131,106,221,55,247,206,198,106,159,24,193
#> 22 109,86,70,169,200,112,237,69,168,97,239,188,150,208,225,190,128,252,142,224
#> 23 161,156,9,65,198,255,245,191,174,63,155,146,13,95,228,100,132,45,49