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Usage

The plugin adds one new function to be able to parse the SAM/BAM/CRAM files correctly. This function is called bam().

bam() function

The function has one mandatory argument:

  • The BAM/CRAM/SAM file used as output of the process/workflow
main.nf.test
then {
    bam("<process or workflow output that contains the SAM/BAM/CRAM file>")
}

The function has one optional argument:

  • The reference FASTA file. This is necessary for some operations on CRAM files.
main.nf.test
then {
    bam("<SAM/BAM/CRAM>", "<reference_fasta>")
}

The fasta can either be a local file or a file URL (currently only supports HTTP and HTTPS protocols)

The function can also be called as sam() or cram(). These are simply aliases of the bam() function and will do exactly the same thing.

Additionally, the stringency option can also be used to set the validation stringency of the HTSJDK library. This can be used to silence the validation errors emitted when an alignment file isn't correct. This options accepts 3 possible values: lenient, silent and strict(default).

main.nf.test
then(
    bam("<SAM/BAM/CRAM>", stringency: "lenient")
)

This will create an AlignmentFile object which has several methods to access the content of the SAM/BAM/CRAM file.

.getHeader() method

The .getHeader() method returns a list of all header lines:

then {
    bam("...").getHeader()
}

[
    "@HD\tVN:1.6\tSO:unsorted",
    "@SQ\tSN:MT192765.1\tLN:29829",
    "@RG\tID:1\tLB:lib1\tPL:ILLUMINA\tSM:test\tPU:barcode1",
    "@PG\tID:minimap2\tPN:minimap2\tVN:2.17-r941\tCL:minimap2 -ax sr tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna tests/data/fastq/dna/sarscov2_1.fastq.gz tests/data/fastq/dna/sarscov2_2.fastq.gz",
    "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.11\tCL:samtools view -Sb sarscov2_aln.sam"
]

.getHeaderMD5() method

The .getHeaderMD5() method returns the MD5 checksum of the header:

then {
    bam("...").getHeaderMD5()
}

"4ab674cd5f921b2b5c68642aeb0ab3f4"

.getReads() method

A reference is needed here for CRAM files

The .getReads() method returns a list of all raw reads from the alignment file:

then {
    bam("...").getReads()
}

[
    "ACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA",
    "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG",
    "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT",
    "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT",
    "TAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAACGTGGTGTGTAAAACTTGTGGACAACAGCAGACAACCCTTAAGGGTGTAGAAGCTGTTATGTAC",
    "TTACAGAGCAAGGGCTGGTGAAGCTGCTAACTTTTGTGCACTTATCTTAGCCTACTGTAATAAGACAGTAGGTGAGTTAGGTGATGTTAGAGAAACAATGAGTTACTTGTTTCAACATGCCAATTTAGATTCTTGCAAAAGAGTCTTGAA",
    "GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG",
    "GTCTACAAGCTGGTAATGCAACAGAAGTGCCTGCCAATTCAACTGTATTATCTTTCTGTGCTTTTGCTGTAGATGCTGCTAAAGCTTACAAAGATTATCTAGCTAGTGGGGGACAACCAATCACTAATTGTG",
    "AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGT",
    "AACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCC",
    "ACTTTCCAAAGTGCAGTCAAAAGAACAATCACGGGTACACACCACTGGTTGTTACTCACAATTTTGACTTCACTTTTAG",
    ...
]

You can also supply an integer to the function to limit the amount of reads the function returns:

then {
    bam("...").getReads(2)
}

[
    "ACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA",
    "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
]

.getReadsMD5() method

The .getReadsMD5() method returns the MD5 checksum of the raw reads:

then {
    bam("...").getReadsMD5()
}

"762e859a3d0ed1553655cde77665c940"

.getSamLines() method

A reference is needed here for CRAM files

The .getSamLines() method returns a list of all lines from the alignment file:

then {
    bam("...").getSamLines()
}

[
    "ERR5069949.2151832\t83\tMT192765.1\t17453\t60\t150M\t=\t17416\t-187\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA<EEEEEEAEEEAEAAAAEEEEEEEEEAAAEE<EEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA\ts1:i:183\ts2:i:0\tRG:Z:1\tAS:i:300\tde:f:0.0\trl:i:0\tcm:i:13\tnn:i:0\ttp:A:P\tms:i:300\n",
    "ERR5069949.2151832\t163\tMT192765.1\t17416\t60\t150M\t=\t17453\t187\tATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG\tAAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE\ts1:i:183\ts2:i:47\tRG:Z:1\tAS:i:300\tde:f:0.0\trl:i:0\tcm:i:14\tnn:i:0\ttp:A:P\tms:i:300\n",
    "ERR5069949.576388\t83\tMT192765.1\t5798\t50\t77M\t=\t5798\t-77\tGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT\tEA/AEEE/<EEEEEEEEEEEAA<EEEEEEEEEEEEEEEEEEEEEAEEEEEAEEEAEE6/EEEAEEEEEEEEEA6AAA\ts1:i:62\ts2:i:0\tRG:Z:1\tAS:i:154\tde:f:0.0\trl:i:0\tcm:i:1\tnn:i:0\ttp:A:P\tms:i:154\n",
    "ERR5069949.576388\t163\tMT192765.1\t5798\t60\t77M\t=\t5798\t77\tGCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT\tAAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE\ts1:i:62\ts2:i:0\tRG:Z:1\tAS:i:154\tde:f:0.0\trl:i:0\tcm:i:10\tnn:i:0\ttp:A:P\tms:i:154\n",
    ...
]

You can also supply an integer to the function to limit the amount of lines the function returns:

then {
    bam("...").getSamLines(2)
}

[
    "ERR5069949.2151832\t83\tMT192765.1\t17453\t60\t150M\t=\t17416\t-187\tACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTGCTGAAATTGTTGACACTGTGAGTGCTTTGGTTTATGA\tAAAA<EEEEEEAEEEAEAAAAEEEEEEEEEAAAEE<EEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAAAAA\ts1:i:183\ts2:i:0\tRG:Z:1\tNM:i:0\tAS:i:300\tde:f:0.0\trl:i:0\tcm:i:13\tnn:i:0\ttp:A:P\tms:i:300\n",
    "ERR5069949.2151832\t163\tMT192765.1\t17416\t60\t150M\t=\t17453\t187\tATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG\tAAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE\ts1:i:183\ts2:i:47\tRG:Z:1\tNM:i:0\tAS:i:300\tde:f:0.0\trl:i:0\tcm:i:14\tnn:i:0\ttp:A:P\tms:i:300\n"
]

.getSamLinesMD5() method

The .getSamLinesMD5() method returns the MD5 checksum of the plain SAM lines:

then {
    bam("...").getSamLinesMD5()
}

"448bf7ab4ce921321beca4ca3bd78f06"

.getFileType() method

The .getFileType() method returns the type ("SAM", "BAM" or "CRAM") of the input file:

then {
    bam("test.bam").getFileType()
}

"BAM"

.getStatistics() method

The .getStatistics() method returns a Map structure containing several statistics for the input file:

then {
    bam("test.bam").getStatistics()
}

{
    "maxReadLength": 151,
    "minReadLength": 53,
    "meanReadLength": 138,
    "maxQuality": 60,
    "minQuality": 0,
    "meanQuality": 57,
    "readCount": 200,
    "duplicateReadCount": 345,
}

This method contains some additional options:

  1. include: this option takes a list of statistic names (the names in the returned map) and returns a map containing these values.
  2. exclude: this option takes a list of statistic names and returns a map without these values.

Examples:

then {
    bam("test.bam").getStatistics(include:["readCount","meanQuality"])
}

then {
    bam("test.bam").getStatistics(exclude:["maxReadLength","minReadLength"])
}

Supplying a s3:// reference

The plugin also supports s3:// for the reference fasta file. By default nft-bam will look at the region us-east-1 unless specified in the ~/.aws/credentials file or in system environment variables. Non-public buckets will need to have the correct permissions set.

main.nf.test
then {
    bam("test.bam", "s3://bucket-name/reference.fasta")
}

Examples

Have a look at the plugin tests to see some example implementations.