# HG changeset patch
# User iuc
# Date 1725013453 0
# Node ID e41d3ce2ab9f8f991400ebdda8638dfe6a668178
# Parent e63aab0f18c629e829d948613c68b290e1b603c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit e3de8bc1123bf4ce56818f2b7ad4b53080cb3bd8
diff -r e63aab0f18c6 -r e41d3ce2ab9f macros.xml
--- a/macros.xml Mon Aug 15 09:13:14 2022 +0000
+++ b/macros.xml Fri Aug 30 10:24:13 2024 +0000
@@ -5,7 +5,14 @@
+
1.15.1
+ 220.05
-
- @misc{SAM_def,
- title={Definition of SAM/BAM format},
- url = {https://samtools.github.io/hts-specs/},}
-
- 10.1093/bioinformatics/btp352
- 10.1093/bioinformatics/btr076
- 10.1093/bioinformatics/btr509
-
- @misc{Danecek_et_al,
- Author={Danecek, P., Schiffels, S., Durbin, R.},
- title={Multiallelic calling model in bcftools (-m)},
- url = {http://samtools.github.io/bcftools/call-m.pdf},}
-
-
- @misc{Durbin_VCQC,
- Author={Durbin, R.},
- title={Segregation based metric for variant call QC},
- url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
-
-
- @misc{Li_SamMath,
- Author={Li, H.},
- title={Mathematical Notes on SAMtools Algorithms},
- url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
-
-
- @misc{SamTools_github,
- title={SAMTools GitHub page},
- url = {https://github.com/samtools/samtools},}
-
+ 10.1093/gigascience/giab008
diff -r e63aab0f18c6 -r e41d3ce2ab9f samtools_view.xml
--- a/samtools_view.xml Mon Aug 15 09:13:14 2022 +0000
+++ b/samtools_view.xml Fri Aug 30 10:24:13 2024 +0000
@@ -1,4 +1,4 @@
-
+- reformat, filter, or subsample SAM, BAM or CRAMmacros.xml
@@ -136,6 +136,9 @@
#if $mode.filter_config.qname_file:
#set std_filters = $std_filters + " --qname-file '%s'" % $mode.filter_config.qname_file
#end if
+ #if str($cond_expr.select_expr) == "yes":
+ #set std_filters = $std_filters + " -e '%s'" % $cond_expr.expression
+ #end if
#end if
#if $with_subsampling:
@@ -154,11 +157,11 @@
## not dealing with all of the reads in the indexed
## file. We have to do an extra pass over the input to
## count the reads to subsample.
- sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
+ sample_fragment=`samtools view -c $std_filters infile $reg_filters | awk '{s=\$1} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
#else:
## We can get the count of reads to subsample using
## an inexpensive call to idxstats.
- sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", frac > 1 ? $seed+1/frac : ".0")}'` &&
+ sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {fac=s/${mode.subsample_config.subsampling_mode.target}; printf("%.8f\n", fac > 1 ? 1/fac : 1)}'` &&
#end if
#end if
#end if
@@ -170,14 +173,14 @@
## filter options (except regions filter, which is the last parameter)
$std_filters
-
#if $with_subsampling:
+ --subsample-seed $seed
#if str($mode.subsample_config.subsampling_mode.select_subsample) == "target":
##this is calculated at execution time before the main samtools command
- -s \${sample_fragment}
+ --subsample \${sample_fragment}
#else:
- #set $fraction = $seed + 1 / float($mode.subsample_config.subsampling_mode.factor)
- -s $fraction
+ #set $fraction = 1 / float($mode.subsample_config.subsampling_mode.factor)
+ --subsample $fraction
#end if
#end if
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**What it does**
@@ -990,12 +1055,143 @@
This filters based on the MAPQ column of the SAM format which gives an estimate about the correct placement of the alignment. Note that aligners do not follow a consistent definition.
-## Filtering by Tag **
+**Filtering by Tag**
This filter allows to select reads based on tool or user specific tags, e.g., XS:i:-18 the alignment score tag of bowtie.
Thus to filter for a specific value of the tag you need the format STR1:STR2, e.g., XS:-18 to filter reads with an aligment score of -18.
You can also just write STR1 without the value STR2 hence the filter selects all reads with the tag STR1, e.g., XS.
+**Filtering by Expression**
+
+
+Filter expressions are used as an on-the-fly checking of incoming SAM, BAM or CRAM records, discarding records that do not match the specified expression.
+
+The language used is primarily C style, but with a few differences in the precedence rules for bit operators and the inclusion of regular expression
+matching.
+
+The operator precedence, from strongest binding to weakest, is
+
+::
+
+ Grouping (, ) E.g. "(1+2)*3"
+ Values: literals, vars Numbers, strings and variables
+ Unary ops: +, -, !, ~ E.g. -10 +10, !10 (not), ~5 (bit not)
+ Math ops: \*, /, % Multiply, division and (integer) modulo
+ Math ops: +, - Addition / subtraction
+ Bit-wise: & Integer AND
+ Bit-wise ^ Integer XOR
+ Bit-wise | Integer OR
+ Conditionals: >, >=, <, <=
+ Equality: \=\=, !=, =~, !~ =~ and !~ match regular expressions
+ Boolean: &&, || Logical AND / OR
+
+
+Expressions are computed using floating point mathematics, so "10 / 4" evaluates to 2.5 rather than 2. They may be written as integers in decimal or
+"0x" plus hexadecimal, and floating point with or without exponents.However operations that require integers first do an implicit type conversion, so
+"7.9 % 5" is 2 and "7.9 & 4.1" is equivalent to "7 & 4", which is 4. Strings are always specified using double quotes. To get a double quote in a
+string, use backslash. Similarly a double backslash is used to get a literal backslash. For example ab\"c\\d is the string ab"c\d.
+
+Comparison operators are evaluated as a match being 1 and a mismatch being 0, thus "(2 > 1) + (3 < 5)" evaluates as 2. All comparisons involving undefined (null) values are deemed to be false.
+
+The variables are where the file format specifics are accessed from the expression. The variables correspond to SAM fields, for example to find paired
+alignments with high mapping quality and a very large insert size, we may use the expression "mapq >= 30 && (tlen >= 100000 || tlen <= -100000)". Valid
+variable names and their data types are:
+
+::
+
+ endpos int Alignment end position (1-based)
+ flag int Combined FLAG field
+ flag.paired int Single bit, 0 or 1
+ flag.proper_pair int Single bit, 0 or 2
+ flag.unmap int Single bit, 0 or 4
+ flag.munmap int Single bit, 0 or 8
+ flag.reverse int Single bit, 0 or 16
+ flag.mreverse int Single bit, 0 or 32
+ flag.read1 int Single bit, 0 or 64
+ flag.read2 int Single bit, 0 or 128
+ flag.secondary int Single bit, 0 or 256
+ flag.qcfail int Single bit, 0 or 512
+ flag.dup int Single bit, 0 or 1024
+ flag.supplementary int Single bit, 0 or 2048
+ hclen int Number of hard-clipped bases
+ library string Library (LB header via RG)
+ mapq int Mapping quality
+ mpos int Synonym for pnext
+ mrefid int Mate reference number (0 based)
+ mrname string Synonym for rnext
+ ncigar int Number of cigar operations
+ pnext int Mate's alignment position (1-based)
+ pos int Alignment position (1-based)
+ qlen int Alignment length: no. query bases
+ qname string Query name
+ qual string Quality values (raw, 0 based)
+ refid int Integer reference number (0 based)
+ rlen int Alignment length: no. reference bases
+ rname string Reference name
+ rnext string Mate's reference name
+ sclen int Number of soft-clipped bases
+ seq string Sequence
+ tlen int Template length (insert size)
+ [XX] int / string XX tag value
+
+
+Flags are returned either as the whole flag value or by checking for a single bit. Hence the filter expression flag.dup is equivalent to flag & 1024.
+
+"qlen" and "rlen" are measured using the CIGAR string to count the number of query (sequence) and reference bases consumed. Note "qlen" may not exactly
+match the length of the "seq" field if the sequence is "*".
+
+"sclen" and "hclen" are the number of soft and hard-clipped bases respectively. The formula "qlen-sclen" gives the number of sequence bases used in the
+alignment, distinguishing between global alignment and local alignment length.
+
+"endpos" is the (1-based inclusive) position of the rightmost mapped base of the read, as measured using the CIGAR string, and for mapped reads is
+equivalent to "pos+rlen-1". For unmapped reads, it is the same as "pos".
+
+Reference names may be matched either by their string forms ("rname" and "mrname") or as the Nth @SQ line (counting from zero) as stored in BAM using
+"tid" and "mtid" respectively.
+
+Auxiliary tags are described in square brackets and these expand to either integer or string as defined by the tag itself (XX:Z:string or XX:i:int).
+For example [NM]>=10 can be used to look for alignments with many mismatches and [RG]=~"grp[ABC]-" will match the read-group string.
+
+If no comparison is used with an auxiliary tag it is taken simply to be a test for the existence of that tag. So [NM] will return any record containing
+an NM tag, even if that tag is zero (NM:i:0). In htslib <= 1.15 negating this with ![NM] gave misleading results as it was true if the tag did not exist
+or did exist but was zero. Now this is strictly does-not-exist. An explicit exists([NM]) and !exists([NM]) function has also been added to make
+this intention clear.
+
+Similarly in htslib <= 1.15 using [NM]!=0 was true both when the tag existed and was not zero as well as when the tag did not exist. From 1.16 onwards
+all comparison operators are only true for tags that exist, so [NM]!=0 works as expected.
+
+Some simple functions are available to operate on strings. These treat the strings as arrays of bytes, permitting their length, minimum, maximum and
+average values to be computed. These are useful for processing Quality Scores.
+
+::
+
+ length(x) Length of the string (excluding nul char)
+ min(x) Minimum byte value in the string
+ max(x) Maximum byte value in the string
+ avg(x) Average byte value in the string
+
+
+Note that "avg" is a floating point value and it may be NAN for empty strings. This means that "avg(qual)" does not produce an error for records that
+have both seq and qual of "*". NAN values will fail any conditional checks, so e.g. "avg(qual) > 20" works and will not report these records. NAN also
+fails all equality, < and > comparisons, and returns zero when given as an argument to the exists function. It can be negated with !x in which case it
+becomes true.
+
+Functions that operate on both strings and numerics:
+
+::
+
+ exists(x) True if the value exists (or is explicitly true).
+ default(x,d) Value x if it exists or d if not.
+
+Functions that apply only to numeric values:
+
+::
+
+ qrt(x) Square root of x
+ og(x) Natural logarithm of x
+ ow(x, y) Power function, x to the power of y
+ xp(x) Base-e exponential, equivalent to pow(e,x)
+
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_1.bam
Binary file test-data/test_1.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_11.sam
--- a/test-data/test_11.sam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_11.sam Fri Aug 30 10:24:13 2024 +0000
@@ -4,7 +4,7 @@
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom!
@PG ID:1 PN:Hey! VN:2.0
-@PG ID:samtools PN:samtools PP:1 VN:1.12 CL:samtools view -@ 0 -h -o outfile infile
+@PG ID:samtools PN:samtools PP:1 VN:1.15.1 CL:samtools view -@ 0 -h -o outfile infile
both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_12.sam
--- a/test-data/test_12.sam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_12.sam Fri Aug 30 10:24:13 2024 +0000
@@ -4,4 +4,4 @@
@SQ SN:chr8 LN:202
@RG ID:0 SM:Hi,Mom!
@PG ID:1 PN:Hey! VN:2.0
-@PG ID:samtools PN:samtools PP:1 VN:1.12 CL:samtools view -H -o outfile infile
+@PG ID:samtools PN:samtools PP:1 VN:1.15.1 CL:samtools view -H -o outfile infile
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_15.cram
Binary file test-data/test_15.cram has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_17.bam
Binary file test-data/test_17.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_19.bam
Binary file test-data/test_19.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_2.bam
Binary file test-data/test_2.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_20.bam
Binary file test-data/test_20.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_21.sam
--- a/test-data/test_21.sam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_21.sam Fri Aug 30 10:24:13 2024 +0000
@@ -3,6 +3,6 @@
@RG ID:UNKNOWN SM:UNKNOWN
@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5
@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2
-@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 1 -h -f 0 -F 0 -G 0 -s 5.20000000 -o outfile infile
-SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA 0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
-SRR065390.6905811 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #######################BB@>A@@BCCB@=BACBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 24733 --subsample 0.20000000 -o outfile infile
+SRR065390.3743423 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ##################?6@:7<=@3=@ABAAB>BDBBABADABDDDBDDBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
+SRR065390.5238868 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA @,=@@D8D;?BBB>;?BBB==BB@D;>D>BBB>BBDDB:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU
SRR065390.1871511 16 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA 0:BB@>B<=B@???@=8@B>BB@CA@DACDCBBCCCA@CCCCACCBCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 XS:i:0 YT:Z:UU
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_23.sam
--- a/test-data/test_23.sam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_23.sam Fri Aug 30 10:24:13 2024 +0000
@@ -4,4 +4,4 @@
@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5
@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2
@PG ID:samtools PN:samtools PP:0 VN:1.12 CL:samtools view -@ 0 -h -s .0 -o outfile infile
-@PG ID:samtools.1 PN:samtools PP:samtools VN:1.12 CL:samtools view -@ 0 -h -s .0 -o outfile infile
+@PG ID:samtools.1 PN:samtools PP:samtools VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 23916 --subsample 1.00000000 -o outfile infile
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_24.bam
Binary file test-data/test_24.bam has changed
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_25.sam
--- a/test-data/test_25.sam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_25.sam Fri Aug 30 10:24:13 2024 +0000
@@ -3,7 +3,7 @@
@RG ID:UNKNOWN SM:UNKNOWN
@PG ID:bowtie2 PN:bowtie2 VN:2.0.0-beta5
@PG ID:0 CL:aaaaa/aaa/aaaaa/aaaaaa/aaaaaaaaa/aaa/iuc/package_aaaaaaaaa_x_y/aaaaaaaaaaaa/bin/aaaaaaaaaaaaaaaaa aaaaaaaaaa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.cram aa /aaaa/aaaaa/aaa/aaaaaaaaaaaaaaaaaaa/tools/aaaaaaaaa/test-data/test.fa -O test PN:samtools VN:1.2
-@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 1 -h -f 0 -F 0 -G 0 -s 7.20000000 -o outfile infile
+@PG ID:samtools PN:samtools PP:0 VN:1.15.1 CL:samtools view -@ 0 -h -f 0 -F 0 -G 0 --subsample-seed 7 --subsample 0.20000000 -o outfile infile
SRR065390.14978392 16 CHROMOSOME_I 2 1 27M1D73M * 0 0 CCTAGCCCTAACCCTAACCCTAACCCTAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA #############################@B?8B?BA@@DDBCDDCBC@CDCDCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC RG:Z:UNKNOWN XG:i:1 XM:i:5 XN:i:0 XO:i:1 AS:i:-18 XS:i:-18 YT:Z:UU
SRR065390.921023 16 CHROMOSOME_I 3 12 100M * 0 0 CTAAGCCTAAATCTAAGCCTAACCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA ###############################################???88:;98768700000<>:BBA?BBAB?BBBBBBBB>B>BB::;?:00000 RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-13 YT:Z:UU
SRR065390.6023338 0 CHROMOSOME_I 3 1 100M * 0 0 CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAAGCTAC CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC@CCDDDBCCABB=DABBA?################ RG:Z:UNKNOWN XG:i:0 XM:i:3 XN:i:0 XO:i:0 AS:i:-6 XS:i:-6 YT:Z:UU
diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_26.bam
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diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_27.bam
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diff -r e63aab0f18c6 -r e41d3ce2ab9f test-data/test_8.bam
--- a/test-data/test_8.bam Mon Aug 15 09:13:14 2022 +0000
+++ b/test-data/test_8.bam Fri Aug 30 10:24:13 2024 +0000
@@ -167,7 +167,7 @@
@SQ SN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT LN:0
@SQ SN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT LN:0
@SQ SN:TTCTTCCCCC LN:0
-@PG ID:samtools PN:samtools VN:1.12 CL:samtools view -@ 0 -h -o outfile infile
+@PG ID:samtools PN:samtools VN:1.15.1 CL:samtools view -@ 0 -h -o outfile infile
HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27