| sam | A complete SAM data set that can be contained in a SAM file. See http://samtools.github.io/hts... |
|---|---|
| sam-alignment | A single read alignment with mandatory and optional fields that can be contained in a SAM file al... |
| sam-header | The information stored in the header section of a SAM file. See http://samtools.github.io/hts... |
| *number-of-threads* | The number of threads used by run-pipeline and run-pipeline-in-situ to parallelize the filtering ... |
|---|---|
| *reference-fai* | The reference FAI that samtools may need for generating a CRAM file. |
| *reference-fasta* | The reference FASTA that samtools may need for generating a CRAM file. |
| *sam-alignment-line-output-length-factor* | Default factor for increase in length of the string representing a sam-alignment instance after a... |
| *sam-file-format-date* | The date of the SAM file format version supported by this library. See http://samtools.github.... |
| *sam-file-format-version* | The SAM file format version string supported by this library. This is entered by default in a ... |
| +default-chunk-size+ | The number of alignments to read from an input source at a time. Default is 8192. |
|---|---|
| +duplicate+ | Bit value for sam-alignment-flag: PCR or optical duplicate. See http://samtools.github.io/hts-... |
| +first+ | Bit value for sam-alignment-flag: the first segment in the template. See http://samtools.githu... |
| +last+ | Bit value for sam-alignment-flag: the last segment in the template. See http://samtools.github... |
| +multiple+ | Bit value for sam-alignment-flag: template having multiple segments in sequencing. See http://... |
| +next-reversed+ | Bit value for sam-alignment-flag: SEQ of the next segment in the template being reversed. See ... |
| +next-unmapped+ | Bit value for sam-alignment-flag: next segment in the template unmapped. See http://samtools.g... |
| +proper+ | Bit value for sam-alignment-flag: each segment properly aligned according to the aligner. See ... |
| +qc-failed+ | Bit value for sam-alignment-flag: not passing quality controls. See http://samtools.github.io/... |
| +reversed+ | Bit value for sam-alignment-flag: SEQ being reversed complemented. See http://samtools.github.... |
| +secondary+ | Bit value for sam-alignment-flag: secondary alignment. See http://samtools.github.io/hts-specs... |
| +supplementary+ | Bit value for sam-alignment-flag: supplementary alignment. See http://samtools.github.io/hts-s... |
| +unmapped+ | Bit value for sam-alignment-flag: segment unmapped. See http://samtools.github.io/hts-specs/SA... |
| add-or-replace-read-group | A filter for adding or replacing the read group both in sam-header and each sam-alignment. |
|---|---|
| add-pg-line | A filter for adding a @PG tag to a sam-header, and ensuring that it is the first one in the chain... |
| add-refid | A filter for adding the refid (index in the reference sequence dictionary) to sam-alignment insta... |
| check-refid-type | Ensure that value is probably an int32. |
| check-stdin | Return true if pathname represents stdin. |
| check-stdout | Return true if pathname represents stdout. |
| chunk-output-loop | Abstract loop for writing chunks of alignments. Each chunk has a sequence number prepended to it.... |
| clean-sam | A filter for soft-clipping a sam-alignment at the end of a reference sequence, and set MAPQ to 0 ... |
| close-sam | Close the stream for a SAM/BAM/CRAM file, and the optional process representation for samtools. ... |
| compose-global-filters | Compose global (header) filters, and return thread-local filters, a global initialization thunk, ... |
| compose-thread-filters | Compose thread-local filters, and return alignment filters, a thread-local initialization thunk, ... |
| compute-phred-score | Sum the adapted Phred qualities of a sam-alignment. |
| compute-unclipped-position | Compute unclipped position of a sam-alignment, based on its POS and CIGAR string. |
| coordinate< | Compare two alignments according to their coordinate. See http://samtools.github.io/hts-specs/... |
| effective-sorting-order | Determine effective sorting order: Some filters may destroy the sorting order recorded in the inp... |
| elprep-script | Command line script for elPrep. |
| estimate-sam-alignment-output-length | Make an estimate how much longer the string will be representing this sam-alignment instance, ... |
| explain-flag | Return a symbolic representation of the FLAG entry in a SAM file alignment line. This is prima... |
| filter-duplicate-reads | A filter for removing duplicate sam-alignment instances, based on FLAG. |
| filter-optional-header-info | A filter for removing header entries that represent optional information in elPrep. |
| filter-optional-reads | A filter for removing sam-alignment instances that represent optional information in elPrep. |
| filter-unmapped-reads | A filter for removing unmapped sam-alignment instances, based on FLAG. |
| filter-unmapped-reads-strict | A filter for removing unmapped sam-alignment instances, based on FLAG, or POS=0, or RNAME=*. |
| format-sam | Write a complete SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1. |
| format-sam-alignment | Write a SAM file read alignment line. See http://samtools.github.io/hts-specs/SAMv1.pdf - Sect... |
| format-sam-byte-array | Write a SAM file TAG of type byte array. See http://samtools.github.io/hts-specs/SAMv1.pdf - S... |
| format-sam-comments | Write the @CO lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| format-sam-datetime | Write a SAM file TAG of type date/time. See http://samtools.github.io/hts-specs/SAMv1.pdf - Se... |
| format-sam-header | Write a SAM file header section. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| format-sam-header-line | Write an @HD line in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv1.... |
| format-sam-header-user-tag | Write a user-defined SAM file TAG of type string. |
| format-sam-integer | Write a SAM file TAG of type integer. |
| format-sam-programs | Write the @PG lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| format-sam-read-groups | Write the @RG lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| format-sam-reference-sequence-dictionary | Write the @SQ lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| format-sam-string | Write a SAM file TAG of type string. |
| format-sam-tag | Write a SAM file TAG, dispatching on actual type of the given value. See http://samtools.githu... |
| format-sam-user-tags | Write the user-defined header lines. See http://samtools.github.io/hts-specs/SAMv1.pdf - Secti... |
| get-samtools | Determine location of the samtools binary. |
| invoke-with-open-sam | Call a function and pass it a stream for reading or writing a SAM file. |
| make-sam | Default constructor for struct sam. |
| make-sam-alignment | Default constructor for struct sam-alignment. |
| make-sam-header | Default constructor for struct sam-header. |
| make-scanner | Create a scanner to scan/parse strings of type simple-base-string. Takes an optional string to sc... |
| mark-duplicates | A filter for marking duplicate sam-alignment instances. Depends on the add-refid filter being cal... |
| merge-sorted-files-split-per-chromosome | A function for merging files that were split with elPrep and sorted in coordinate order. |
| open-sam | Open a SAM file for :input or :output. If the file is .bam or .cram, use samtools view for input ... |
| open-temporary-sam | Open a temporary SAM file for :output in the same folder as the sibling file. If the file is .bam... |
| parse-read-group-from-string | Parse an @RG line in a string. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1.3... |
| parse-sam | Parse a complete SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1. |
| parse-sam-alignment | Parse a SAM file read alignment line. See http://samtools.github.io/hts-specs/SAMv1.pdf - Sect... |
| parse-sam-byte-array | Parse a byte array in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section ... |
| parse-sam-comment | Parse an @CO line in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| parse-sam-header | Parse a SAM file header section. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| parse-sam-header-line | Parse an @HD line in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| parse-sam-numeric-array | Parse a numeric array in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Secti... |
| parse-sam-program | Parse an @PG line in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| parse-sam-read-group | Parse an @RG line in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| parse-sam-reference-sequence-dictionary-entry | Parse an @SQ line in a SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| replace-reference-sequence-dictionary | A filter for replacing the reference sequence dictionary in a sam-header. |
| replace-reference-sequence-dictionary-from-sam-file | A filter for replacing the reference sequence dictionary in a sam-header with one parsed from the... |
| sam-alignment-cigar | Access the sam-alignment CIGAR string of type base-string. |
| sam-alignment-duplicate-p | Check for PCR or optical duplicate in sam-alignment-flag. See http://samtools.github.io/hts-sp... |
| sam-alignment-first-p | Check for being the first segment in the template in sam-alignment-flag. See http://samtools.g... |
| sam-alignment-flag | Access the sam-alignment bitwise FLAG of type fixnum. |
| sam-alignment-flag-every | Check for every bit in flag being set in sam-alignment-flag. |
| sam-alignment-flag-notany | Check for not any bit in flag being set in sam-alignment-flag. |
| sam-alignment-flag-notevery | Check for not every bit in flag being set in sam-alignment-flag. |
| sam-alignment-flag-some | Check for some bits in flag being set in sam-alignment-flag. |
| sam-alignment-last-p | Check for being the last segment in the template in sam-alignment-flag. See http://samtools.gi... |
| sam-alignment-mapq | Access the sam-alignment MAPping quality of type fixnum. |
| sam-alignment-multiple-p | Check for template having multiple segments in sequencing in sam-alignment-flag. See http://sa... |
| sam-alignment-next-reversed-p | Check for SEQ of the next segment in the template being reversed in sam-alignment-flag. See ht... |
| sam-alignment-next-unmapped-p | Check for next segment in the template unmapped in sam-alignment-flag. See http://samtools.git... |
| sam-alignment-p | Default predicate for struct sam-alignment. |
| sam-alignment-pnext | Access the sam-alignment 1-based leftmost mapping Position of the mate/NEXT read of type int32. |
| sam-alignment-pos | Access the sam-alignment 1-based leftmost mapping POSition of type int32. |
| sam-alignment-proper-p | Check for each segment being properly aligned according to the aligner in sam-alignment-flag. ... |
| sam-alignment-qc-failed-p | Check for not passing quality controls in sam-alignment-flag. See http://samtools.github.io/ht... |
| sam-alignment-qname | Access the sam-alignment Query template NAME of type base-string. |
| sam-alignment-qual | Access the sam-alignment ASCII of Phred-scaled base QUALity+33 of type base-string. |
| sam-alignment-refid | Access the commonly used REFID temporary field in the sam-alignment. |
| sam-alignment-reversed-p | Check for SEQ being reversed complemented in sam-alignment-flag. See http://samtools.github.io... |
| sam-alignment-rg | Access the read group optional field of a sam-alignment. |
| sam-alignment-rname | Access the sam-alignment Reference sequence NAME of type base-string. |
| sam-alignment-rnext | Access the sam-alignment Reference sequence name of the mate/NEXT read of type base-string. |
| sam-alignment-secondary-p | Check for secondary alignment in sam-alignment-flag. See http://samtools.github.io/hts-specs/S... |
| sam-alignment-seq | Access the sam-alignment segment SEQuence of type base-string. |
| sam-alignment-supplementary-p | Check for supplementary alignment in sam-alignment-flag. See http://samtools.github.io/hts-spe... |
| sam-alignment-tag | Access a sam-alignment optional field in the sam-alignment. |
| sam-alignment-tags | Access the sam-alignment optional fields of type property list. |
| sam-alignment-temp | Access a sam-alignment temporary value in the sam-alignment. |
| sam-alignment-temps | Access the sam-alignment temporary values of type property list. |
| sam-alignment-tlen | Access the sam-alignment observed Template LENgth of type int32. |
| sam-alignment-unmapped-p | Check for segment unmapped in sam-alignment-flag. See http://samtools.github.io/hts-specs/SAMv... |
| sam-alignments | Access the sam list of sam-alignment instances. |
| sam-file-kind | Determine whether the file is :bam for .bam, :cram for .cram, or :sam in all other cases. |
| sam-header | Access the sam header of type sam-header. |
| sam-header-co | Access the sam-header @CO lines of type list of strings. |
| sam-header-ensure-hd | Ensure an @HD line is present in the given sam-header. See http://samtools.github.io/hts-specs... |
| sam-header-hd | Access the sam-header @HD line of type property list. |
| sam-header-p | Default predicate for struct sam-header. |
| sam-header-pg | Access the sam-header @PG lines of type list of property lists. |
| sam-header-rg | Access the sam-header @RG lines of type list of property lists. |
| sam-header-sq | Access the sam-header @SQ lines of type list of property lists. |
| sam-header-user-tag | Access a sam-header user tag. |
| sam-header-user-tag-p | Does this tag string represent a user-defined tag? |
| sam-header-user-tags | Access the sam-header user-defined header lines of type property list. |
| sam-p | Default predicate for struct sam. |
| scan-cigar-string | Convert a cigar string to an association 'list or 'vector. See http://samtools.github.io/hts-s... |
| scan-float | Scan a floating point number from scanner. Returns either an integer or a single-float. |
| scan-integer | Scan an integer from scanner. |
| scan-string | Read a tab-delimited entry as string from scanner. |
| setup-standard-streams | Bind standard streams to standard error. |
| skip-sam-header | Skip the SAM file header section. |
| split-file-per-chromosome | A function for splitting a sam file into : a file containing all unmapped reads, a file containin... |
| create-chunk-filter | Combines an optional alignment input mapper, a list of alignment filters, and an optional output ... |
|---|---|
| get-output-functions | Sets up the output thread, feeds the given header to the output data set, and returns four functi... |
| run-pipeline | Reads a SAM data set from input, applies filters to the header and the alignments, and writes... |
| run-pipeline-in-situ | Applies filters destructively and returns the first argument. This is like run-pipeline, exce... |
| with-alignment-filters | Macro version of compose-thread-filters. |
|---|---|
| with-chunk-output | Macro version of chunk-output-loop. |
| with-open-sam | Macro version of invoke-with-open-sam. |
| with-output-functions | Macro for receiving results from get-output-functions. |
| with-thread-filters | Macro version of compose-global-filters. |