| bounded-mailbox | A mailbox with an upper bound on the number of objects that can be simultaneously present. Add... |
|---|---|
| buffer | A buffer can be used to create simple-base-strings that can grow arbitrarily large in size. It... |
| handle | An indirection for compare-and-swap operations. The struct handle has a constructor make-handl... |
| pair | A pair consisting of two fragment sam-alignment instances. The struct pair has a constructor m... |
| process | This struct represents the return values of sys:run-shell-command in LispWorks. It has defau... |
| 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... |
| scanner | A scanner to scan/parse string of type simple-base-string. The struct scanner has a constructo... |
| sim-stream | A pseudo string stream to allow for more low-level efficient implementations of formatting functi... |
| simple-tree | A simple balanced tree. The struct simple-tree has a constructor that takes the rank and optio... |
| split-hash-table | A collection of hash tables distributing the entries based on a permutation of the same hash func... |
| temporary-file | An internal representation for temporary files. The struct temporary-file has a constructor ma... |
| *cigar-consumes-reference-bases-table* | Map CIGAR operations to boolean flags indicating whether they consume reference bases. |
|---|---|
| *cigar-list-cache* | Cache CIGAR Strings to association lists. See http://samtools.github.io/hts-specs/SAMv1.pdf - ... |
| *cigar-operations* | Map CIGAR operations represented as characters to upcase characters. See http://samtools.githu... |
| *cigar-vector-cache* | Cache CIGAR strings to assocation vectors. See http://samtools.github.io/hts-specs/SAMv1.pdf -... |
| *fixnum-optimization* | Standard optimizations settings with fixnum optimizations. |
| *integer-types* | Integer types supported in SAM file numeric arrays. See http://samtools.github.io/hts-specs/... |
| *keyword* | The :keyword package. |
| *merge-program-help* | Help string for the elprep-merge-script binary. |
| *number-of-threads* | The number of threads used by run-pipeline and run-pipeline-in-situ to parallelize the filtering ... |
| *optimization* | Standard optimization settings without fixnum optimizations. |
| *program-help* | Help string for the elprep-script binary. |
| *program-name* | Name of the elprep binary. |
| *program-url* | URL for more information about elprep. |
| *program-version* | Version of the elprep binary. |
| *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 ... |
| *samtools* | Location of the samtools binary. |
| *split-program-help* | Help string for the elprep-split-script binary. |
| *stderr* | Standard error stream of the underlying Common Lisp implementation. |
| *unique-value* | A unique value for use in the functions presentp and unique. |
| +buffer-chunk-size+ | Size of buffer chunks. |
|---|---|
| +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... |
| +high-bits+ | An arbitrary number of bits in the high portion of a fixnum, used for split hash tables. |
| +highest-bits+ | Bit mask for the highest bits of a fixnum, used for split hash tables. |
| +last+ | Bit value for sam-alignment-flag: the last segment in the template. See http://samtools.github... |
| +low-bits+ | An arbitrary number of bits in the low portion of a fixnum, used for split hash tables. |
| +lowest-bits+ | Bit mask for the lowest bits of a fixnum, used for split hash tables. |
| +max-cigar-operation+ | The largest CIGAR operation. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1.4.6... |
| +max-optional-field-type-tag+ | The largest optional field type tag. See http://samtools.github.io/hts-specs/SAMv1.pdf - Secti... |
| +max-upcase-cigar-operation+ | The largest CIGAR operation, upper case only. See http://samtools.github.io/hts-specs/SAMv1.pd... |
| +min-cigar-operation+ | The smallest CIGAR operation. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1.4.... |
| +min-optional-field-type-tag+ | The smallest optional field type tag. See http://samtools.github.io/hts-specs/SAMv1.pdf - Sect... |
| +min-upcase-cigar-operation+ | The smallest CIGAR operation, upper case only. See http://samtools.github.io/hts-specs/SAMv1.p... |
| +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... |
| +total-bits+ | Number of bits that make up a fixnum in the current Common Lisp implementation. |
| +unmapped+ | Bit value for sam-alignment-flag: segment unmapped. See http://samtools.github.io/hts-specs/SA... |
| %compose-filters | Low-level filter composition, used by compose-global-filters and compose-thread-filters. |
|---|---|
| %make-buffer | Default constructor for struct buffer. |
| %make-split-hash-table | Constructor for struct split-hash-table that takes a hash function and a vector of splits as para... |
| %open-sam | Open a SAM file for :input or :output. If kind is :bam or :cram, use samtools view for input or o... |
| adapt-alignment | Adapt the sam-alignment: Make read group unique; fill in unclipped position; fill in Phred score. |
| 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... |
| advance | Advance scanner by one character if possible. |
| bounded-mailbox-mailbox | Read the bounded-mailbox underlying actual mailbox. |
| bounded-mailbox-p | Default predicate for struct bounded-mailbox. |
| bounded-mailbox-semaphore | Read the bounded-mailbox semaphore that controls the number of elements that are present in the m... |
| buffer-copy | Copy the active contents of one buffer to another. |
| buffer-emptyp | Returns true if the active size of the buffer is 0. |
| buffer-extend | Add a base-string to a buffer. |
| buffer-hash | Get the hash code for a buffer; once a hash code is computed, the buffer shouldn't change anymore... |
| buffer-hash-value | The hash-value for the active contents of a buffer. If -1, the hash-value hasn't been computed ye... |
| buffer-p | Default predicate for struct buffer. |
| buffer-parse-integer | Parse a buffer as an integer. |
| buffer-partition | Get substrings from a buffer and feed them to target buffers after reinitializing them; separa... |
| buffer-pos | The current active size of a buffer. |
| buffer-push | Add a single character to a buffer. |
| buffer-str | An array of string chunks holding the contents of a buffer. |
| buffer-string | Return a string representation of the active contents of a buffer. Use this only for debugging... |
| buffer= | Compare the active contents of two buffers. |
| call-with-threads | Set up the filter threads for a filter pipeline, and execute the input thread. |
| check-file-sorting-order | Assert that no sorting is asked for files. |
| 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.... |
| cigar-aux-pos | Position in a vector of CIGAR operations, starting with the smallest CIGAR operation, upper case ... |
| classify-fragment | For each list of sam-alignment instances with the same unclipped position and direction, all exce... |
| classify-pair | For each list of pairs with the same unclipped positions and directions, all except the one with ... |
| 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. ... |
| command-line-arguments | Wrapper for sys:*line-arguments-list* in LispWorks, and sb-ext:*posix-argv* in SBCL. |
| common-number-type | Determine the smallest numeric type supported by SAM file numeric arrays that can represent all n... |
| compare-sam-files | A function for comparing two sam files. The input files must be sorted by coordinate order. |
| compare-sams | Parse both SAM files, then compare the mandatory fields of all alignments one by one. |
| 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, ... |
| compose-thunks | Return a single thunk that executes the given thunks in sequence. |
| 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/... |
| copy-bounded-mailbox | Default copier function for struct bounded-mailbox. |
| copy-handle | Default copier function for struct handle. |
| copy-pair | Default copier function for struct pair. |
| copy-process | Default copier for struct process. |
| copy-sam | Default copier function for struct sam. |
| copy-sam-alignment | Default copier function for struct sam-header. |
| copy-sam-header | Default copier function for struct sam-header. |
| copy-sim-stream | Default copier function for struct sim-stream. |
| copy-simple-tree | Default copier function for struct simple-tree. |
| copy-split-hash-table | Default copier function for struct split-hash-table. |
| copy-stream | Efficient copying of the contents of a buffered-stream to an output stream. |
| copy-temporary-file | Default copier function for struct temporary-file. |
| count-duplicates | Return the number of alignments in the SAM file that are marked as duplicates. |
| create-log-filename | Create a log filename for writing error messages from within the elPrep binary. |
| effective-sorting-order | Determine effective sorting order: Some filters may destroy the sorting order recorded in the inp... |
| element-stradless-clipped-read | |
| elprep-debugger-hook | Write an error report to a log file and exist the elPrep binary. |
| elprep-filter-script | Command line script for elprep filter script. |
| elprep-merge-script | Command line script for elprep merge script. |
| elprep-script | Command line script for elPrep. |
| elprep-split-script | Command line script for elprep split script. |
| end-of-entry-p | Is the character a tab or end of line, delimiting an entry in a tab-delimited text file? |
| ensure-chunk | Ensure that buffer-str has enough chunks (internal). |
| ensure-sim-space | Ensure there is enough space in the target string of sim-stream out, with length additional chara... |
| ensure-str | Ensure that buffer-str holds enough chunks (internal). |
| 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... |
| fast-scan-cigar-string-to-list | Convert a cigar string to an association list, fast path. See http://samtools.github.io/hts-sp... |
| fast-scan-cigar-string-to-vector | Convert a cigar string to an association vector, fast path. See http://samtools.github.io/hts-... |
| filter | Filter out each element from the list, optionally bounded by tail, for which filter returns nil. |
| 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=*. |
| filtermap | Apply the following steps to each element in the list, optionally bounded by tail: - Filter ou... |
| 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... |
| fragment-hash | Hash function that corresponds to handle-fragment=, but operates an a sam-alignment directly. |
| get-function | Get a function object from a function (returned as is) or a function name. |
| get-read-length-from-cigar | Sums the lengths of all CIGAR operations that consume read bases. |
| get-samtools | Determine location of the samtools binary. |
| handle-fragment= | Do the two handles refer to sam-alignment instances at the same unclipped position and with the s... |
| handle-hash | Read the handle hash value of type fixnum. |
| handle-object | Access the handle object. |
| handle-p | Default predicate for struct handle. |
| handle-pair= | Do the two handles refer to pair instances at the same unclipped positions and with the same dire... |
| hash-table-split | Return a split of a split-hash-table for a given key. |
| insert-node | Insert a node into the given simple-tree. Returns the tree unless it is fully occupied. If it ... |
| intern-key | Intern a string in the :keyword package. |
| intern-key/copy | Find a symbol in the :keyword package or, if not found, intern a copy of the string in the :keywo... |
| invoke-with-open-sam | Call a function and pass it a stream for reading or writing a SAM file. |
| make-bounded-mailbox | Constructor for struct bounded-mailbox that takes a capacity as a parameter. |
| make-buffer | Create a buffer with an optional initial string |
| make-cigar-operation | Parse a CIGAR length + operation from position i in the cigar string. Return a cons cell with ... |
| make-cigar-operations-table | Map CIGAR operations represented as characters to upcase characters. See http://samtools.githu... |
| make-cigar-operations-table-consumes-reference-bases | Map CIGAR operations to boolean flags indicating whether they consume reference bases. |
| make-handle | Constructor for struct handle that takes an object and a hash value as parameters. |
| make-integer-type-descriptors | Create descriptors for the integer types in SAM file numeric arrays. Types with smaller inde... |
| make-mailbox | Create a mailbox. If the optional capacity parameter is provided and is not nil, then a bounded-m... |
| make-optional-field-scan-table | Create a dispatch table for scanning optional fields in a SAM file read alignment line. See ht... |
| make-pair | Constructor for struct pair that takes a score and two sam-alignment instances as parameters. |
| make-phred-score-table | Map Phred qualities to a reasonable range and an error flag indicating if it is outside a valid r... |
| make-process | Default constructor for struct process. |
| 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... |
| make-sim-stream | Constructor for struct sim-stream that takes an optional initial size for the target string as a ... |
| make-simple-tree | Constructor for struct simple-tree that takes the rank and optionally the depth as parameters. |
| make-single-thread-hash-table | Like make-hash-table, but ensure it is single-thread, not synchronized. |
| make-split-hash-table | Constructor for split-hash-table that takes the number of splits and initialization arguments as ... |
| make-subtree | Create a subtree for the given simple-tree. |
| make-super-tree | Create a super tree for the given simple-tree, and add the given tree to the new super tree as it... |
| make-synchronized-hash-table | Like make-hash-table, but ensure it is synchronized, not single-thread. |
| make-temporary-file | Constructor for struct temporary-file that takes a sibling file as a parameter. |
| make-unclipped-aux-tables | Map CIGAR operations to flags indicating whether they are clipped and/or reference operations, up... |
| mapcar* | Like mapcar, except operates on only one list, optionally bounded by tail. |
| mapfilter | Apply the following steps to each element in the list, optionally bounded by tail: - Apply map... |
| mapfiltermap | Apply the following steps to each element in the list, optionally bounded by tail: - Apply inm... |
| mark-as-duplicate | Set the PCR/optical duplicate FLAG in the sam-alignment. |
| 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. |
| merge-unsorted-files-split-per-chromosome | A function for merging files that were split with elPrep and are unsorted |
| nfilter | Destructively filter out each element from the list, optionally bounded by tail, for which filter... |
| nfiltermap | Destructively apply the following steps to each element in the list, optionally bounded by tail: ... |
| nmapcar* | Like mapcar, except destructively operates on only one list, optionally bounded by tail. |
| nmapfilter | Destructively apply the following steps to each element in the list, optionally bounded by tail: ... |
| nmapfiltermap | Destructively apply the following steps to each element in the list, optionally bounded by tail: ... |
| nthdiff | Return a copy of the first n elements of list, and the nth cdr of the list. |
| 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... |
| operator-consumes-read-bases-p | Does the CIGAR operation consume read bases? |
| operator-consumes-reference-bases-p | Does the CIGAR operation consume reference bases? |
| pair-aln1 | Read the first fragment of type sam-alignment from a pair. |
| pair-aln2 | Read the second fragment of type sam-alignment from a pair. |
| pair-hash | Hash function that corresponds to handle-pair=, but operates on a pair directly. |
| pair-p | Default predicate for struct pair. |
| pair-pos1 | Access the first unclipped position of a pair. |
| pair-pos2 | Access the second unclipped position of a pair. |
| pair-refid1 | Access the first REFID of a pair. |
| pair-refid2 | Access the second REFID of a pair. |
| pair-reversed1-p | Access the first direction of a pair. |
| pair-reversed2-p | Access the second direction of a pair. |
| pair-rg | Access the read group of a pair. |
| pair-score | Read the pair score of type fixnum. |
| 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-alignment-from-stream | Read a line from a stream and parse it as a SAM alignment line. Return NIL if stream is at end... |
| 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-code | Parse the record type code of a SAM header line. |
| 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... |
| parse-sam-tag | Parse the TAG: portion of a SAM file tag. |
| peekc | Peek current character in scanner if possible, or return #EOT. |
| presentp | Is the indicator present in the property list? |
| process-close | Close all streams of an external process, wait for the process to finish if requested, and return... |
| process-error | The error stream of an external process. |
| process-input | Returns the result of process-stream. Exists for compatibility with SBCL's sb-ext:process-input. |
| process-output | Returns the result of process-stream. Exists for compatibility with SBCL's sb-ext:process-output. |
| process-p | Default predicate for struct process. |
| process-pid | The PID of an external process. |
| process-stream | The stream of an external process. |
| read-line-into-buffer | Read a line from a stream into a buffer, after reinitializing it. |
| readc | Read current character in scanner if possible, or return #EOT. |
| real-diffs | Return a list of sam-alignments in alns1 for which no alignments in alns2 exist that have the sam... |
| reference-sequence-length | Get reference sequence length for the given sam-alignment. |
| reinitialize-buffer | Reset buffer-pos and buffer-hash-value, so this buffer can be reused. |
| reinitialize-scanner | Reinitialize the scanner so it can be reused. |
| rename-chromosomes | A filter for prepending “chr” to the reference sequence names in a sam-header, and in RNAME and R... |
| 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... |
| rotate-1 | Rotate a fixnum by one position. |
| rotate-15 | Rotate a fixnum by 15 bits, used for split hash tables. |
| run-best-practices-pipeline | Run the best practices pipeline. Version that doesn't use an intermediate list when neither sorti... |
| run-best-practices-pipeline-intermediate-list | Run the best practices pipeline. Version that uses an intermediate list so that sorting and mark-... |
| run-program | A wrapper for sys:run-shell-command in LispWorks to make it behave more like SBCL's sb-ext:run-pr... |
| sam-alignment-adapted-pos | Access the unclipped position temporary field in the sam-alignment. |
| sam-alignment-adapted-score | Access adapted Phred score temporary field in the sam-alignment. |
| sam-alignment-cigar | Access the sam-alignment CIGAR string of type base-string. |
| sam-alignment-differ | Return false if the two sam-alignments have the same mandatory fields. Otherwise, return a sym... |
| sam-alignment-duplicate-p | Check for PCR or optical duplicate in sam-alignment-flag. See http://samtools.github.io/hts-sp... |
| sam-alignment-end | Sums the lengths of all CIGAR operations that consume reference bases. |
| 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-line | |
| 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-pair-hash | Hash function that corresponds to sam-alignment-pair=. |
| sam-alignment-pair= | Are the two sam-alignment fragments part of the same pair? |
| 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-same | Return true if the two sam-alignments have the same mandatory fields, false otherwise. |
| 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-error | Signal invalid type tag for optional field in SAM alignment. |
| 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. |
| scanc | Read current character in scanner, ensuring it is the given one. |
| scanner-index | The current index into the string while scanning/parsing it. |
| scanner-string | The string being scanned/parsed. |
| set buffer-hash-value | |
| set buffer-pos | |
| set buffer-str | |
| set handle-object | |
| set sam-alignment-cigar | |
| set sam-alignment-flag | |
| set sam-alignment-line | |
| set sam-alignment-mapq | |
| set sam-alignment-pnext | |
| set sam-alignment-pos | |
| set sam-alignment-qname | |
| set sam-alignment-qual | |
| set sam-alignment-rname | |
| set sam-alignment-rnext | |
| set sam-alignment-seq | |
| set sam-alignment-tags | |
| set sam-alignment-temps | |
| set sam-alignment-tlen | |
| set sam-alignments | |
| set sam-header | |
| set sam-header-co | |
| set sam-header-hd | |
| set sam-header-pg | |
| set sam-header-rg | |
| set sam-header-sq | |
| set sam-header-user-tags | |
| set scanner-index | |
| set scanner-string | |
| set sim-stream-%floats | |
| set sim-stream-index | |
| set sim-stream-string | |
| set simple-tree-index | |
| set temporary-file-sibling | |
| setup-standard-streams | Bind standard streams to standard error. |
| sim-format-sam | Write a complete SAM file. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1. |
| sim-format-sam-alignment | Write a SAM file read alignment line. See http://samtools.github.io/hts-specs/SAMv1.pdf - Sect... |
| sim-format-sam-byte-array | Write a SAM file TAG of type byte array. See http://samtools.github.io/hts-specs/SAMv1.pdf - S... |
| sim-format-sam-comments | Write the @CO lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| sim-format-sam-datetime | Write a SAM file TAG of type date/time. See http://samtools.github.io/hts-specs/SAMv1.pdf - Se... |
| sim-format-sam-header | Write a SAM file header section. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1... |
| sim-format-sam-header-line | Write an @HD line in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv1.... |
| sim-format-sam-header-user-tag | Write a user-defined SAM file TAG of type string. |
| sim-format-sam-integer | Write a SAM file TAG of type integer. |
| sim-format-sam-programs | Write the @PG lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| sim-format-sam-read-groups | Write the @RG lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| sim-format-sam-reference-sequence-dictionary | Write the @SQ lines in a SAM file header section. See http://samtools.github.io/hts-specs/SAMv... |
| sim-format-sam-string | Write a SAM file TAG of type string. |
| sim-format-sam-tag | Write a SAM file TAG, dispatching on actual type of the given value. See http://samtools.githu... |
| sim-format-sam-user-tags | Write the user-defined header lines. See http://samtools.github.io/hts-specs/SAMv1.pdf - Secti... |
| sim-stream-%floats | Access the optional sim-stream string-stream for formatting floating point numbers. |
| sim-stream-floats | Read the sim-stream string-stream for formatting floating point numbers, creating a new one if no... |
| sim-stream-index | Access the sim-stream index into sim-stream-string. |
| sim-stream-p | Default predicate for struct sim-stream. |
| sim-stream-string | Access the sim-stream target string. |
| sim-write-byte | Write a byte in hex notation to sim-stream out. |
| sim-write-fixed-size-fixnum | Write a positive fixnum of known maximum width to sim-stream out. |
| sim-write-float | Write a floating point number to sim-stream out. |
| sim-write-integer | Write a decimal integer to sim-stream out. |
| sim-write-newline | Write a newline to sim-stream out. |
| sim-write-tab | Write a tab to sim-stream out. |
| sim-writec | Write a character c to sim-stream out. |
| sim-writestr | Write a string to sim-stream out. |
| simple-tree-depth | Read the simple-tree depth of type fixnum. |
| simple-tree-index | Access the simple-tree index of type fixnum. |
| simple-tree-nodes | Read the simple-tree nodes of type simple-vector. |
| simple-tree-p | Default predicate for struct simple-tree. |
| simple-tree-rank | Read the simple-tree rank of type fixnum. |
| skip-line | Skip characters from stream until a newline is reached. Can be used in place of read-line wh... |
| skip-sam-header | Skip the SAM file header section. |
| slow-buffer-extend | Add a simple-base-string to a buffer (internal slow path). |
| slow-ensure-sim-space | Ensure there is enough space in the target string of sim-stream out at index with a required-leng... |
| slow-scan-cigar-string-to-list | Convert a cigar string to an association list, slow path. See http://samtools.github.io/hts-sp... |
| slow-scan-cigar-string-to-vector | Convert a cigar string to an assocation vector, slow path. See http://samtools.github.io/hts-s... |
| soft-clip-end-of-read | |
| sorting-criterion | Determine sorting criterion for given sorting order, which is a list of parameters to be passed t... |
| split-file-per-chromosome | A function for splitting a sam file into : a file containing all unmapped reads, a file containin... |
| split-hash-table-hash-function | Read the split-hash-table hash function. |
| split-hash-table-p | Default predicate for struct split-hash-table. |
| split-hash-table-vector | Read the split-hash-table vector of splits of type simple-vector. |
| temporary-file-p | Default predicate for struct temporary-file. |
| temporary-file-sibling | Access the temporary-file sibling. |
| thread-join | Similar to LispWorks's mp:process-join. |
| thread-run | Wrapper around mp:process-run-function in LispWorks, and sb-thread:make-thread in SBCL. |
| tree-reduce | Perform a parallel map/reduce traversal over the given simple-tree. |
| true-fragment-p | Is this sam-alignment definitely not part of a pair? |
| true-pair-p | Is this sam-alignment definitely part of a pair? |
| unique | Assert that the indicator is not present in the property list. |
| unwrap-displaced-array | Unwrap a displaced array and return the underlying actual array and an offset into that array whi... |
| verify-order-kept | Assume the SAM file is sorted by coordinate order. Verify that this is stil the case. |
| write-buffer | Write the active contents of a buffer to a stream |
| write-newline | Write a newline to an output stream. |
| write-tab | Write a tabulator to an output stream. |
| writec | Write a character to an output stream. |
| writeln | Write a simple-base-string to an output stream, but only up to a #Newline. |
| writestr | Write a base-string to an output stream. |
| 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... |
| mailbox-read | Read an object from a mailbox. May block if there are no objects in the mailbox. |
| mailbox-send | Send an object to a mailbox. |
| 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... |
| defglobal | Define a global variable. |
|---|---|
| in-simple-base-string-syntax | Make literal strings produce simple-base-string instead of (array character (*)) in SBCL. |
| unwind-protectn | Like unwind-protect, except that all forms but the last are protected, and only the last form is ... |
| with-alignment-filters | Macro version of compose-thread-filters. |
| with-ascii-stream-input-buffer | Specialize a body of code for different types of a buffered-ascii-input-stream's input buffer in ... |
| with-buffer-dispatch | Specialize a body of code for different types of buffers in SBCL. |
| with-chunk-output | Macro version of chunk-output-loop. |
| with-modify-hash | Macro version of LispWorks's modify-hash function. |
| with-open-sam | Macro version of invoke-with-open-sam. |
| with-output-functions | Macro for receiving results from get-output-functions. |
| with-prepared-header | Prepare the header for further processing, when input is in memory. |
| with-sam-chunk | Access the components of a chunk of sam-alignment instances. |
| with-thread-filters | Macro version of compose-global-filters. |