diff --git a/constants/BAM.yaml b/constants/BAM.yaml new file mode 100644 index 00000000..b3a7822a --- /dev/null +++ b/constants/BAM.yaml @@ -0,0 +1,16 @@ +constants: +- name: magic + value: 'BAM\\1' + +outputs: + python: + path: autogenerated/python/BAM.py + javascript: + path: autogenerated/javascript/BAM.js + c: + path: autogenerated/c/BAM.h + java: + path: autogenerated/java/BAM.java + rust: + path: autogenerated/rust/BAM.rs + diff --git a/constants/SAM.yaml b/constants/SAM.yaml new file mode 100644 index 00000000..9f9b601e --- /dev/null +++ b/constants/SAM.yaml @@ -0,0 +1,157 @@ +constants: +- name: SAM_HEADER_TAG + value: "HD" + description: The tag for the SAM header +- name: SAM_HEADER_VERSION_TAG + value: VN + description: The version tag for the SAM header +- name: SAM_HEADER_SORTORDER_TAG + value: SO + description: The sort order tag for the SAM header +- name: SAM_HEADER_GROUPORDER_TAG + value: GO + description: The group order tag for the SAM header +- name: SAM_HEADER_SUBSORT_TAG + value: SS + description: The subsort tag for the SAM header +- name: SAM_HEADER_REFERENCE_SEQUENCE + value: SQ + description: The reference sequence tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_LENGTH + value: LN + description: The sequence length tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_ALTERNATIVE + value: AH + description: Is alternative sequence tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME + value: AN + description: The alternative sequence names tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_ASSEMBLY_ID + value: AS + description: The assembly ID tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_DESCRIPTION + value: DS + description: The sequence description tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_MD5 + value: M5 + description: The MD5 tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_SPECIES + value: SP + description: The species tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_TOPOLOGY + value: TP + description: The topology tag for the SAM header sequence +- name: SAM_HEADER_SEQUENCE_URI + value: UR + description: The URI tag for the SAM header sequence +- name: SAM_HEADER_READGROUP_TAG + value: RG + description: The read group tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_ID + value: ID + description: The read group ID tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_BARCODE + value: BC + description: The read group barcode tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_SEQ_CENTER + value: SC + description: The sequencing center tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_DESCRIPTION + value: DS + description: The description tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_DATE + value: DT + description: The date tag for the SAM header readgroup +- name: SAM_HEADER_READGROUP_FLOWORDER + value: FO +- name: SAM_HEADER_READGROUP_KEY_SEQUENCE + value: KS +- name: SAM_HEADER_READGROUP_LIBRARY + value: LB +- name: SAM_HEADER_READGROUP_PROGRAMS + value: PG +- name: SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE + value: PI +- name: SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY + value: PL +- name: SAM_HEADER_READGROUP_PLATFORM_MODEL + value: PM +- name: SAM_HEADER_READGROUP_PLATFORM_UNIT + value: PU +- name: SAM_HEADER_READGROUP_SAMPLE + value: SM +- name: SAM_FLAG_MULTIPLE + value: 1 +- name: SAM_FLAG_ALL_PROPERLY_ALIGNED + value: 2 +- name: SAM_FLAG_PROPERLY_PAIRED + value: 2 +- name: SAM_FLAG_SEGMENT_UNMAPPED + value: 4 +- name: SAM_FLAG_NEXT_SEGMENT_UNMAPPED + value: 8 +- name: SAM_FLAG_MATE_UNMAPPED + value: 8 +- name: SAM_FLAG_CURRENT_REVERSE_STRAND + value: 16 +- name: SAM_FLAG_NEXT_REVERSE_STRAND + value: 32 +- name: SAM_FLAG_MATE_REVERSE_STRAND + value: 32 +- name: SAM_FLAG_FIRST_SEGMENT + value: 64 +- name: SAM_FLAG_READ1 + value: 64 +- name: SAM_FLAG_LAST_SEGMENT + value: 128 +- name: SAM_FLAG_READ2 + value: 128 +- name: SAM_FLAG_SECONDARY_ALIGNMENT + value: 256 +- name: SAM_FLAG_NOT_PASSING_FILTERS + value: 512 +- name: SAM_FLAG_DUPLICATE + value: 1024 +- name: SAM_FLAG_SUPPLEMENTARY_ALIGNMENT + value: 2048 + +enums: + - name: SAM_HEADER_SORT_ORDER_TYPE + values: + - unknown + - coordinate + - queryname + - strand + - name: SAM_HEADER_SUBSORT + values: + - lexicographical + - natural + - umi + - name: SAM_HEADER_RG_PLATFORM + values: + - CAPILLARY + - DNBSEQ + - ELEMENT + - HELICOS + - ILLUMINA + - IONTORRENT + - LS454 + - ONT + - PACBIO + - SINGULAR + - SOLID + - ULTIMA + + +outputs: + python: + path: autogenerated/python/SAM.py + javascript: + path: autogenerated/javascript/SAM.js + c: + path: autogenerated/c/SAM.h + java: + path: autogenerated/java/SAM.java + rust: + path: autogenerated/rust/SAM.rs + diff --git a/constants/SamTags.yaml b/constants/SamTags.yaml new file mode 100644 index 00000000..67adc06d --- /dev/null +++ b/constants/SamTags.yaml @@ -0,0 +1,269 @@ +constants: +- name: SAM_TAG_AM + value: "AM" + type: "i" + description: The smallest template-independent mapping quality in the template +- name: SAM_TAG_AS + value: "AS" + type: "i" + description: Alignment score generated by aligner +- name: SAM_TAG_BC + value: "BC" + type: "Z" + description: Barcode sequence identifying the sample +- name: SAM_TAG_BQ + value: "BQ" + type: "Z" + description: Offset to base alignment quality (BAQ) +- name: SAM_TAG_BZ + value: "BZ" + type: "Z" + description: Phred quality of the unique molecular barcode bases in the {\tt OX} tag +- name: SAM_TAG_CB + value: "CB" + type: "Z" + description: Cell identifier +- name: SAM_TAG_CC + value: "CC" + type: "Z" + description: Reference name of the next hit +- name: SAM_TAG_CG + value: "CG" + type: "B" + description: 'BAM only: {\sf CIGAR} in BAMs binary encoding if (and only if) it consists of $>$65535 operators' +- name: SAM_TAG_CM + value: "CM" + type: "i" + description: Edit distance between the color sequence and the color reference (see also {\tt NM}) +- name: SAM_TAG_CO + value: "CO" + type: "Z" + description: Free-text comments +- name: SAM_TAG_CP + value: "CP" + type: "i" + description: Leftmost coordinate of the next hit +- name: SAM_TAG_CQ + value: "CQ" + type: "Z" + description: Color read base qualities +- name: SAM_TAG_CR + value: "CR" + type: "Z" + description: Cellular barcode sequence bases (uncorrected) +- name: SAM_TAG_CS + value: "CS" + type: "Z" + description: Color read sequence +- name: SAM_TAG_CT + value: "CT" + type: "Z" + description: Complete read annotation tag, used for consensus annotation dummy features +- name: SAM_TAG_CY + value: "CY" + type: "Z" + description: Phred quality of the cellular barcode sequence in the {\tt CR} tag +- name: SAM_TAG_E2 + value: "E2" + type: "Z" + description: The 2nd most likely base calls +- name: SAM_TAG_FI + value: "FI" + type: "i" + description: The index of segment in the template +- name: SAM_TAG_FS + value: "FS" + type: "Z" + description: Segment suffix +- name: SAM_TAG_FZ + value: "FZ" + type: "B" + description: Flow signal intensities +- name: SAM_TAG_GC + value: "GC" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_GQ + value: "GQ" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_GS + value: "GS" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_H0 + value: "H0" + type: "i" + description: Number of perfect hits +- name: SAM_TAG_H1 + value: "H1" + type: "i" + description: Number of 1-difference hits (see also {\tt NM}) +- name: SAM_TAG_H2 + value: "H2" + type: "i" + description: Number of 2-difference hits +- name: SAM_TAG_HI + value: "HI" + type: "i" + description: Query hit index +- name: SAM_TAG_IH + value: "IH" + type: "i" + description: Query hit total count +- name: SAM_TAG_LB + value: "LB" + type: "Z" + description: Library +- name: SAM_TAG_MC + value: "MC" + type: "Z" + description: CIGAR string for mate/next segment +- name: SAM_TAG_MD + value: "MD" + type: "Z" + description: String encoding mismatched and deleted reference bases +- name: SAM_TAG_MF + value: "MF" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_MI + value: "MI" + type: "Z" + description: Molecular identifier; a string that uniquely identifies the molecule from which the record was derived +- name: SAM_TAG_ML + value: "ML" + type: "B" + description: Base modification probabilities +- name: SAM_TAG_MM + value: "MM" + type: "Z" + description: 'Base modifications / methylation' +- name: SAM_TAG_MN + value: "MN" + type: "i" + description: Length of sequence at the time {\tt MM} and {\tt ML} were produced +- name: SAM_TAG_MQ + value: "MQ" + type: "i" + description: Mapping quality of the mate/next segment +- name: SAM_TAG_NH + value: "NH" + type: "i" + description: Number of reported alignments that contain the query in the current record +- name: SAM_TAG_NM + value: "NM" + type: "i" + description: Edit distance to the reference +- name: SAM_TAG_OA + value: "OA" + type: "Z" + description: Original alignment +- name: SAM_TAG_OC + value: "OC" + type: "Z" + description: Original CIGAR (deprecated; use {\tt OA} instead) + deprecated: true + deprecated_ref: OA +- name: SAM_TAG_OP + value: "OP" + type: "i" + description: Original mapping position (deprecated; use {\tt OA} instead) +- name: SAM_TAG_OQ + value: "OQ" + type: "Z" + description: Original base quality + deprecated: true + deprecated_ref: OA +- name: SAM_TAG_OX + value: "OX" + type: "Z" + description: Original unique molecular barcode bases +- name: SAM_TAG_PG + value: "PG" + type: "Z" + description: Program +- name: SAM_TAG_PQ + value: "PQ" + type: "i" + description: Phred likelihood of the template +- name: SAM_TAG_PT + value: "PT" + type: "Z" + description: Read annotations for parts of the padded read sequence +- name: SAM_TAG_PU + value: "PU" + type: "Z" + description: Platform unit +- name: SAM_TAG_Q2 + value: "Q2" + type: "Z" + description: Phred quality of the mate/next segment sequence in the {\tt R2} tag +- name: SAM_TAG_QT + value: "QT" + type: "Z" + description: Phred quality of the sample barcode sequence in the {\tt BC} tag +- name: SAM_TAG_QX + value: "QX" + type: "Z" + description: Quality score of the unique molecular identifier in the {\tt RX} tag +- name: SAM_TAG_R2 + value: "R2" + type: "Z" + description: Sequence of the mate/next segment in the template +- name: SAM_TAG_RG + value: "RG" + type: "Z" + description: Read group +- name: SAM_TAG_RT + value: "RT" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_RX + value: "RX" + type: "Z" + description: Sequence bases of the (possibly corrected) unique molecular identifier +- name: SAM_TAG_S2 + value: "S2" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_SA + value: "SA" + type: "Z" + description: Other canonical alignments in a chimeric alignment +- name: SAM_TAG_SM + value: "SM" + type: "i" + description: Template-independent mapping quality +- name: SAM_TAG_SQ + value: "SQ" + type: "?" + description: Reserved for backwards compatibility reasons +- name: SAM_TAG_TC + value: "TC" + type: "i" + description: The number of segments in the template +- name: SAM_TAG_TS + value: "TS" + type: "A" + description: Transcript strand +- name: SAM_TAG_U2 + value: "U2" + type: "Z" + description: Phred probability of the 2nd call being wrong conditional on the best being wrong +- name: SAM_TAG_UQ + value: "UQ" + type: "i" + description: 'Phred likelihood of the segment, conditional on the mapping being correct' + +outputs: + python: + path: autogenerated/python/SamTags.py + javascript: + path: autogenerated/javascript/SamTags.js + c: + path: autogenerated/c/SamTags.h + java: + path: autogenerated/java/SamTags.java + rust: + path: autogenerated/rust/SamTags.rs diff --git a/constants/autogenerated/c/BAM.h b/constants/autogenerated/c/BAM.h new file mode 100644 index 00000000..533a7c0a --- /dev/null +++ b/constants/autogenerated/c/BAM.h @@ -0,0 +1,10 @@ +// autogenerated by reconstant - do not edit! +#ifndef AUTOGENERATED_C_BAM_H +#define AUTOGENERATED_C_BAM_H + +// constants +const char* MAGIC = "BAM\\1"; + +// enums + +#endif /* AUTOGENERATED_C_BAM_H */ \ No newline at end of file diff --git a/constants/autogenerated/c/SAM.h b/constants/autogenerated/c/SAM.h new file mode 100644 index 00000000..7a0dc2a7 --- /dev/null +++ b/constants/autogenerated/c/SAM.h @@ -0,0 +1,59 @@ +// autogenerated by reconstant - do not edit! +#ifndef AUTOGENERATED_C_SAM_H +#define AUTOGENERATED_C_SAM_H + +// constants +const char* SAM_HEADER_TAG = "HD"; +const char* SAM_HEADER_VERSION_TAG = "VN"; +const char* SAM_HEADER_SORTORDER_TAG = "SO"; +const char* SAM_HEADER_GROUPORDER_TAG = "GO"; +const char* SAM_HEADER_SUBSORT_TAG = "SS"; +const char* SAM_HEADER_REFERENCE_SEQUENCE = "SQ"; +const char* SAM_HEADER_SEQUENCE_LENGTH = "LN"; +const char* SAM_HEADER_SEQUENCE_ALTERNATIVE = "AH"; +const char* SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME = "AN"; +const char* SAM_HEADER_SEQUENCE_ASSEMBLY_ID = "AS"; +const char* SAM_HEADER_SEQUENCE_DESCRIPTION = "DS"; +const char* SAM_HEADER_SEQUENCE_MD5 = "M5"; +const char* SAM_HEADER_SEQUENCE_SPECIES = "SP"; +const char* SAM_HEADER_SEQUENCE_TOPOLOGY = "TP"; +const char* SAM_HEADER_SEQUENCE_URI = "UR"; +const char* SAM_HEADER_READGROUP_TAG = "RG"; +const char* SAM_HEADER_READGROUP_ID = "ID"; +const char* SAM_HEADER_READGROUP_BARCODE = "BC"; +const char* SAM_HEADER_READGROUP_SEQ_CENTER = "SC"; +const char* SAM_HEADER_READGROUP_DESCRIPTION = "DS"; +const char* SAM_HEADER_READGROUP_DATE = "DT"; +const char* SAM_HEADER_READGROUP_FLOWORDER = "FO"; +const char* SAM_HEADER_READGROUP_KEY_SEQUENCE = "KS"; +const char* SAM_HEADER_READGROUP_LIBRARY = "LB"; +const char* SAM_HEADER_READGROUP_PROGRAMS = "PG"; +const char* SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE = "PI"; +const char* SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY = "PL"; +const char* SAM_HEADER_READGROUP_PLATFORM_MODEL = "PM"; +const char* SAM_HEADER_READGROUP_PLATFORM_UNIT = "PU"; +const char* SAM_HEADER_READGROUP_SAMPLE = "SM"; +const int SAM_FLAG_MULTIPLE = 1; +const int SAM_FLAG_ALL_PROPERLY_ALIGNED = 2; +const int SAM_FLAG_PROPERLY_PAIRED = 2; +const int SAM_FLAG_SEGMENT_UNMAPPED = 4; +const int SAM_FLAG_NEXT_SEGMENT_UNMAPPED = 8; +const int SAM_FLAG_MATE_UNMAPPED = 8; +const int SAM_FLAG_CURRENT_REVERSE_STRAND = 16; +const int SAM_FLAG_NEXT_REVERSE_STRAND = 32; +const int SAM_FLAG_MATE_REVERSE_STRAND = 32; +const int SAM_FLAG_FIRST_SEGMENT = 64; +const int SAM_FLAG_READ1 = 64; +const int SAM_FLAG_LAST_SEGMENT = 128; +const int SAM_FLAG_READ2 = 128; +const int SAM_FLAG_SECONDARY_ALIGNMENT = 256; +const int SAM_FLAG_NOT_PASSING_FILTERS = 512; +const int SAM_FLAG_DUPLICATE = 1024; +const int SAM_FLAG_SUPPLEMENTARY_ALIGNMENT = 2048; + +// enums +typedef enum { unknown, coordinate, queryname, strand } SAM_HEADER_SORT_ORDER_TYPE; +typedef enum { lexicographical, natural, umi } SAM_HEADER_SUBSORT; +typedef enum { CAPILLARY, DNBSEQ, ELEMENT, HELICOS, ILLUMINA, IONTORRENT, LS454, ONT, PACBIO, SINGULAR, SOLID, ULTIMA } SAM_HEADER_RG_PLATFORM; + +#endif /* AUTOGENERATED_C_SAM_H */ \ No newline at end of file diff --git a/constants/autogenerated/c/SamTags.h b/constants/autogenerated/c/SamTags.h new file mode 100644 index 00000000..b806fa22 --- /dev/null +++ b/constants/autogenerated/c/SamTags.h @@ -0,0 +1,72 @@ +// autogenerated by reconstant - do not edit! +#ifndef AUTOGENERATED_C_SAMTAGS_H +#define AUTOGENERATED_C_SAMTAGS_H + +// constants +const char* SAM_TAG_AM = "AM"; +const char* SAM_TAG_AS = "AS"; +const char* SAM_TAG_BC = "BC"; +const char* SAM_TAG_BQ = "BQ"; +const char* SAM_TAG_BZ = "BZ"; +const char* SAM_TAG_CB = "CB"; +const char* SAM_TAG_CC = "CC"; +const char* SAM_TAG_CG = "CG"; +const char* SAM_TAG_CM = "CM"; +const char* SAM_TAG_CO = "CO"; +const char* SAM_TAG_CP = "CP"; +const char* SAM_TAG_CQ = "CQ"; +const char* SAM_TAG_CR = "CR"; +const char* SAM_TAG_CS = "CS"; +const char* SAM_TAG_CT = "CT"; +const char* SAM_TAG_CY = "CY"; +const char* SAM_TAG_E2 = "E2"; +const char* SAM_TAG_FI = "FI"; +const char* SAM_TAG_FS = "FS"; +const char* SAM_TAG_FZ = "FZ"; +const char* SAM_TAG_GC = "GC"; +const char* SAM_TAG_GQ = "GQ"; +const char* SAM_TAG_GS = "GS"; +const char* SAM_TAG_H0 = "H0"; +const char* SAM_TAG_H1 = "H1"; +const char* SAM_TAG_H2 = "H2"; +const char* SAM_TAG_HI = "HI"; +const char* SAM_TAG_IH = "IH"; +const char* SAM_TAG_LB = "LB"; +const char* SAM_TAG_MC = "MC"; +const char* SAM_TAG_MD = "MD"; +const char* SAM_TAG_MF = "MF"; +const char* SAM_TAG_MI = "MI"; +const char* SAM_TAG_ML = "ML"; +const char* SAM_TAG_MM = "MM"; +const char* SAM_TAG_MN = "MN"; +const char* SAM_TAG_MQ = "MQ"; +const char* SAM_TAG_NH = "NH"; +const char* SAM_TAG_NM = "NM"; +const char* SAM_TAG_OA = "OA"; +const char* SAM_TAG_OC = "OC"; +const char* SAM_TAG_OP = "OP"; +const char* SAM_TAG_OQ = "OQ"; +const char* SAM_TAG_OX = "OX"; +const char* SAM_TAG_PG = "PG"; +const char* SAM_TAG_PQ = "PQ"; +const char* SAM_TAG_PT = "PT"; +const char* SAM_TAG_PU = "PU"; +const char* SAM_TAG_Q2 = "Q2"; +const char* SAM_TAG_QT = "QT"; +const char* SAM_TAG_QX = "QX"; +const char* SAM_TAG_R2 = "R2"; +const char* SAM_TAG_RG = "RG"; +const char* SAM_TAG_RT = "RT"; +const char* SAM_TAG_RX = "RX"; +const char* SAM_TAG_S2 = "S2"; +const char* SAM_TAG_SA = "SA"; +const char* SAM_TAG_SM = "SM"; +const char* SAM_TAG_SQ = "SQ"; +const char* SAM_TAG_TC = "TC"; +const char* SAM_TAG_TS = "TS"; +const char* SAM_TAG_U2 = "U2"; +const char* SAM_TAG_UQ = "UQ"; + +// enums + +#endif /* AUTOGENERATED_C_SAMTAGS_H */ \ No newline at end of file diff --git a/constants/autogenerated/java/BAM.java b/constants/autogenerated/java/BAM.java new file mode 100644 index 00000000..efe178e6 --- /dev/null +++ b/constants/autogenerated/java/BAM.java @@ -0,0 +1,9 @@ +// autogenerated by reconstant - do not edit! +public final class BAM { + + // constants + public static final String MAGIC = "BAM\\1"; + + // enums + +} \ No newline at end of file diff --git a/constants/autogenerated/java/SAM.java b/constants/autogenerated/java/SAM.java new file mode 100644 index 00000000..93f7f816 --- /dev/null +++ b/constants/autogenerated/java/SAM.java @@ -0,0 +1,80 @@ +// autogenerated by reconstant - do not edit! +public final class SAM { + + // constants + public static final String SAM_HEADER_TAG = "HD"; + public static final String SAM_HEADER_VERSION_TAG = "VN"; + public static final String SAM_HEADER_SORTORDER_TAG = "SO"; + public static final String SAM_HEADER_GROUPORDER_TAG = "GO"; + public static final String SAM_HEADER_SUBSORT_TAG = "SS"; + public static final String SAM_HEADER_REFERENCE_SEQUENCE = "SQ"; + public static final String SAM_HEADER_SEQUENCE_LENGTH = "LN"; + public static final String SAM_HEADER_SEQUENCE_ALTERNATIVE = "AH"; + public static final String SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME = "AN"; + public static final String SAM_HEADER_SEQUENCE_ASSEMBLY_ID = "AS"; + public static final String SAM_HEADER_SEQUENCE_DESCRIPTION = "DS"; + public static final String SAM_HEADER_SEQUENCE_MD5 = "M5"; + public static final String SAM_HEADER_SEQUENCE_SPECIES = "SP"; + public static final String SAM_HEADER_SEQUENCE_TOPOLOGY = "TP"; + public static final String SAM_HEADER_SEQUENCE_URI = "UR"; + public static final String SAM_HEADER_READGROUP_TAG = "RG"; + public static final String SAM_HEADER_READGROUP_ID = "ID"; + public static final String SAM_HEADER_READGROUP_BARCODE = "BC"; + public static final String SAM_HEADER_READGROUP_SEQ_CENTER = "SC"; + public static final String SAM_HEADER_READGROUP_DESCRIPTION = "DS"; + public static final String SAM_HEADER_READGROUP_DATE = "DT"; + public static final String SAM_HEADER_READGROUP_FLOWORDER = "FO"; + public static final String SAM_HEADER_READGROUP_KEY_SEQUENCE = "KS"; + public static final String SAM_HEADER_READGROUP_LIBRARY = "LB"; + public static final String SAM_HEADER_READGROUP_PROGRAMS = "PG"; + public static final String SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE = "PI"; + public static final String SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY = "PL"; + public static final String SAM_HEADER_READGROUP_PLATFORM_MODEL = "PM"; + public static final String SAM_HEADER_READGROUP_PLATFORM_UNIT = "PU"; + public static final String SAM_HEADER_READGROUP_SAMPLE = "SM"; + public static final int SAM_FLAG_MULTIPLE = 1; + public static final int SAM_FLAG_ALL_PROPERLY_ALIGNED = 2; + public static final int SAM_FLAG_PROPERLY_PAIRED = 2; + public static final int SAM_FLAG_SEGMENT_UNMAPPED = 4; + public static final int SAM_FLAG_NEXT_SEGMENT_UNMAPPED = 8; + public static final int SAM_FLAG_MATE_UNMAPPED = 8; + public static final int SAM_FLAG_CURRENT_REVERSE_STRAND = 16; + public static final int SAM_FLAG_NEXT_REVERSE_STRAND = 32; + public static final int SAM_FLAG_MATE_REVERSE_STRAND = 32; + public static final int SAM_FLAG_FIRST_SEGMENT = 64; + public static final int SAM_FLAG_READ1 = 64; + public static final int SAM_FLAG_LAST_SEGMENT = 128; + public static final int SAM_FLAG_READ2 = 128; + public static final int SAM_FLAG_SECONDARY_ALIGNMENT = 256; + public static final int SAM_FLAG_NOT_PASSING_FILTERS = 512; + public static final int SAM_FLAG_DUPLICATE = 1024; + public static final int SAM_FLAG_SUPPLEMENTARY_ALIGNMENT = 2048; + + // enums + public enum SAM_HEADER_SORT_ORDER_TYPE { + unknown, + coordinate, + queryname, + strand + } + public enum SAM_HEADER_SUBSORT { + lexicographical, + natural, + umi + } + public enum SAM_HEADER_RG_PLATFORM { + CAPILLARY, + DNBSEQ, + ELEMENT, + HELICOS, + ILLUMINA, + IONTORRENT, + LS454, + ONT, + PACBIO, + SINGULAR, + SOLID, + ULTIMA + } + +} \ No newline at end of file diff --git a/constants/autogenerated/java/SamTags.java b/constants/autogenerated/java/SamTags.java new file mode 100644 index 00000000..ce8ff792 --- /dev/null +++ b/constants/autogenerated/java/SamTags.java @@ -0,0 +1,71 @@ +// autogenerated by reconstant - do not edit! +public final class SamTags { + + // constants + public static final String SAM_TAG_AM = "AM"; + public static final String SAM_TAG_AS = "AS"; + public static final String SAM_TAG_BC = "BC"; + public static final String SAM_TAG_BQ = "BQ"; + public static final String SAM_TAG_BZ = "BZ"; + public static final String SAM_TAG_CB = "CB"; + public static final String SAM_TAG_CC = "CC"; + public static final String SAM_TAG_CG = "CG"; + public static final String SAM_TAG_CM = "CM"; + public static final String SAM_TAG_CO = "CO"; + public static final String SAM_TAG_CP = "CP"; + public static final String SAM_TAG_CQ = "CQ"; + public static final String SAM_TAG_CR = "CR"; + public static final String SAM_TAG_CS = "CS"; + public static final String SAM_TAG_CT = "CT"; + public static final String SAM_TAG_CY = "CY"; + public static final String SAM_TAG_E2 = "E2"; + public static final String SAM_TAG_FI = "FI"; + public static final String SAM_TAG_FS = "FS"; + public static final String SAM_TAG_FZ = "FZ"; + public static final String SAM_TAG_GC = "GC"; + public static final String SAM_TAG_GQ = "GQ"; + public static final String SAM_TAG_GS = "GS"; + public static final String SAM_TAG_H0 = "H0"; + public static final String SAM_TAG_H1 = "H1"; + public static final String SAM_TAG_H2 = "H2"; + public static final String SAM_TAG_HI = "HI"; + public static final String SAM_TAG_IH = "IH"; + public static final String SAM_TAG_LB = "LB"; + public static final String SAM_TAG_MC = "MC"; + public static final String SAM_TAG_MD = "MD"; + public static final String SAM_TAG_MF = "MF"; + public static final String SAM_TAG_MI = "MI"; + public static final String SAM_TAG_ML = "ML"; + public static final String SAM_TAG_MM = "MM"; + public static final String SAM_TAG_MN = "MN"; + public static final String SAM_TAG_MQ = "MQ"; + public static final String SAM_TAG_NH = "NH"; + public static final String SAM_TAG_NM = "NM"; + public static final String SAM_TAG_OA = "OA"; + public static final String SAM_TAG_OC = "OC"; + public static final String SAM_TAG_OP = "OP"; + public static final String SAM_TAG_OQ = "OQ"; + public static final String SAM_TAG_OX = "OX"; + public static final String SAM_TAG_PG = "PG"; + public static final String SAM_TAG_PQ = "PQ"; + public static final String SAM_TAG_PT = "PT"; + public static final String SAM_TAG_PU = "PU"; + public static final String SAM_TAG_Q2 = "Q2"; + public static final String SAM_TAG_QT = "QT"; + public static final String SAM_TAG_QX = "QX"; + public static final String SAM_TAG_R2 = "R2"; + public static final String SAM_TAG_RG = "RG"; + public static final String SAM_TAG_RT = "RT"; + public static final String SAM_TAG_RX = "RX"; + public static final String SAM_TAG_S2 = "S2"; + public static final String SAM_TAG_SA = "SA"; + public static final String SAM_TAG_SM = "SM"; + public static final String SAM_TAG_SQ = "SQ"; + public static final String SAM_TAG_TC = "TC"; + public static final String SAM_TAG_TS = "TS"; + public static final String SAM_TAG_U2 = "U2"; + public static final String SAM_TAG_UQ = "UQ"; + + // enums + +} \ No newline at end of file diff --git a/constants/autogenerated/javascript/BAM.js b/constants/autogenerated/javascript/BAM.js new file mode 100644 index 00000000..300c8181 --- /dev/null +++ b/constants/autogenerated/javascript/BAM.js @@ -0,0 +1,6 @@ +// autogenerated by reconstant - do not edit! + +// constants +export const magic = "BAM\\1" + +// enums diff --git a/constants/autogenerated/javascript/SAM.js b/constants/autogenerated/javascript/SAM.js new file mode 100644 index 00000000..ae04bccf --- /dev/null +++ b/constants/autogenerated/javascript/SAM.js @@ -0,0 +1,77 @@ +// autogenerated by reconstant - do not edit! + +// constants +export const SAM_HEADER_TAG = "HD" +export const SAM_HEADER_VERSION_TAG = "VN" +export const SAM_HEADER_SORTORDER_TAG = "SO" +export const SAM_HEADER_GROUPORDER_TAG = "GO" +export const SAM_HEADER_SUBSORT_TAG = "SS" +export const SAM_HEADER_REFERENCE_SEQUENCE = "SQ" +export const SAM_HEADER_SEQUENCE_LENGTH = "LN" +export const SAM_HEADER_SEQUENCE_ALTERNATIVE = "AH" +export const SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME = "AN" +export const SAM_HEADER_SEQUENCE_ASSEMBLY_ID = "AS" +export const SAM_HEADER_SEQUENCE_DESCRIPTION = "DS" +export const SAM_HEADER_SEQUENCE_MD5 = "M5" +export const SAM_HEADER_SEQUENCE_SPECIES = "SP" +export const SAM_HEADER_SEQUENCE_TOPOLOGY = "TP" +export const SAM_HEADER_SEQUENCE_URI = "UR" +export const SAM_HEADER_READGROUP_TAG = "RG" +export const SAM_HEADER_READGROUP_ID = "ID" +export const SAM_HEADER_READGROUP_BARCODE = "BC" +export const SAM_HEADER_READGROUP_SEQ_CENTER = "SC" +export const SAM_HEADER_READGROUP_DESCRIPTION = "DS" +export const SAM_HEADER_READGROUP_DATE = "DT" +export const SAM_HEADER_READGROUP_FLOWORDER = "FO" +export const SAM_HEADER_READGROUP_KEY_SEQUENCE = "KS" +export const SAM_HEADER_READGROUP_LIBRARY = "LB" +export const SAM_HEADER_READGROUP_PROGRAMS = "PG" +export const SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE = "PI" +export const SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY = "PL" +export const SAM_HEADER_READGROUP_PLATFORM_MODEL = "PM" +export const SAM_HEADER_READGROUP_PLATFORM_UNIT = "PU" +export const SAM_HEADER_READGROUP_SAMPLE = "SM" +export const SAM_FLAG_MULTIPLE = 1 +export const SAM_FLAG_ALL_PROPERLY_ALIGNED = 2 +export const SAM_FLAG_PROPERLY_PAIRED = 2 +export const SAM_FLAG_SEGMENT_UNMAPPED = 4 +export const SAM_FLAG_NEXT_SEGMENT_UNMAPPED = 8 +export const SAM_FLAG_MATE_UNMAPPED = 8 +export const SAM_FLAG_CURRENT_REVERSE_STRAND = 16 +export const SAM_FLAG_NEXT_REVERSE_STRAND = 32 +export const SAM_FLAG_MATE_REVERSE_STRAND = 32 +export const SAM_FLAG_FIRST_SEGMENT = 64 +export const SAM_FLAG_READ1 = 64 +export const SAM_FLAG_LAST_SEGMENT = 128 +export const SAM_FLAG_READ2 = 128 +export const SAM_FLAG_SECONDARY_ALIGNMENT = 256 +export const SAM_FLAG_NOT_PASSING_FILTERS = 512 +export const SAM_FLAG_DUPLICATE = 1024 +export const SAM_FLAG_SUPPLEMENTARY_ALIGNMENT = 2048 + +// enums +export const SAM_HEADER_SORT_ORDER_TYPE = { + unknown : 0, + coordinate : 1, + queryname : 2, + strand : 3, +} +export const SAM_HEADER_SUBSORT = { + lexicographical : 0, + natural : 1, + umi : 2, +} +export const SAM_HEADER_RG_PLATFORM = { + CAPILLARY : 0, + DNBSEQ : 1, + ELEMENT : 2, + HELICOS : 3, + ILLUMINA : 4, + IONTORRENT : 5, + LS454 : 6, + ONT : 7, + PACBIO : 8, + SINGULAR : 9, + SOLID : 10, + ULTIMA : 11, +} diff --git a/constants/autogenerated/javascript/SamTags.js b/constants/autogenerated/javascript/SamTags.js new file mode 100644 index 00000000..b4316f1d --- /dev/null +++ b/constants/autogenerated/javascript/SamTags.js @@ -0,0 +1,68 @@ +// autogenerated by reconstant - do not edit! + +// constants +export const SAM_TAG_AM = "AM" +export const SAM_TAG_AS = "AS" +export const SAM_TAG_BC = "BC" +export const SAM_TAG_BQ = "BQ" +export const SAM_TAG_BZ = "BZ" +export const SAM_TAG_CB = "CB" +export const SAM_TAG_CC = "CC" +export const SAM_TAG_CG = "CG" +export const SAM_TAG_CM = "CM" +export const SAM_TAG_CO = "CO" +export const SAM_TAG_CP = "CP" +export const SAM_TAG_CQ = "CQ" +export const SAM_TAG_CR = "CR" +export const SAM_TAG_CS = "CS" +export const SAM_TAG_CT = "CT" +export const SAM_TAG_CY = "CY" +export const SAM_TAG_E2 = "E2" +export const SAM_TAG_FI = "FI" +export const SAM_TAG_FS = "FS" +export const SAM_TAG_FZ = "FZ" +export const SAM_TAG_GC = "GC" +export const SAM_TAG_GQ = "GQ" +export const SAM_TAG_GS = "GS" +export const SAM_TAG_H0 = "H0" +export const SAM_TAG_H1 = "H1" +export const SAM_TAG_H2 = "H2" +export const SAM_TAG_HI = "HI" +export const SAM_TAG_IH = "IH" +export const SAM_TAG_LB = "LB" +export const SAM_TAG_MC = "MC" +export const SAM_TAG_MD = "MD" +export const SAM_TAG_MF = "MF" +export const SAM_TAG_MI = "MI" +export const SAM_TAG_ML = "ML" +export const SAM_TAG_MM = "MM" +export const SAM_TAG_MN = "MN" +export const SAM_TAG_MQ = "MQ" +export const SAM_TAG_NH = "NH" +export const SAM_TAG_NM = "NM" +export const SAM_TAG_OA = "OA" +export const SAM_TAG_OC = "OC" +export const SAM_TAG_OP = "OP" +export const SAM_TAG_OQ = "OQ" +export const SAM_TAG_OX = "OX" +export const SAM_TAG_PG = "PG" +export const SAM_TAG_PQ = "PQ" +export const SAM_TAG_PT = "PT" +export const SAM_TAG_PU = "PU" +export const SAM_TAG_Q2 = "Q2" +export const SAM_TAG_QT = "QT" +export const SAM_TAG_QX = "QX" +export const SAM_TAG_R2 = "R2" +export const SAM_TAG_RG = "RG" +export const SAM_TAG_RT = "RT" +export const SAM_TAG_RX = "RX" +export const SAM_TAG_S2 = "S2" +export const SAM_TAG_SA = "SA" +export const SAM_TAG_SM = "SM" +export const SAM_TAG_SQ = "SQ" +export const SAM_TAG_TC = "TC" +export const SAM_TAG_TS = "TS" +export const SAM_TAG_U2 = "U2" +export const SAM_TAG_UQ = "UQ" + +// enums diff --git a/constants/autogenerated/python/BAM.py b/constants/autogenerated/python/BAM.py new file mode 100644 index 00000000..c18bbe37 --- /dev/null +++ b/constants/autogenerated/python/BAM.py @@ -0,0 +1,7 @@ +# autogenerated by reconstant - do not edit! +from enum import Enum + +# constants +magic = "BAM\\1" + +# enums diff --git a/constants/autogenerated/python/SAM.py b/constants/autogenerated/python/SAM.py new file mode 100644 index 00000000..12c595ca --- /dev/null +++ b/constants/autogenerated/python/SAM.py @@ -0,0 +1,78 @@ +# autogenerated by reconstant - do not edit! +from enum import Enum + +# constants +SAM_HEADER_TAG = "HD" +SAM_HEADER_VERSION_TAG = "VN" +SAM_HEADER_SORTORDER_TAG = "SO" +SAM_HEADER_GROUPORDER_TAG = "GO" +SAM_HEADER_SUBSORT_TAG = "SS" +SAM_HEADER_REFERENCE_SEQUENCE = "SQ" +SAM_HEADER_SEQUENCE_LENGTH = "LN" +SAM_HEADER_SEQUENCE_ALTERNATIVE = "AH" +SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME = "AN" +SAM_HEADER_SEQUENCE_ASSEMBLY_ID = "AS" +SAM_HEADER_SEQUENCE_DESCRIPTION = "DS" +SAM_HEADER_SEQUENCE_MD5 = "M5" +SAM_HEADER_SEQUENCE_SPECIES = "SP" +SAM_HEADER_SEQUENCE_TOPOLOGY = "TP" +SAM_HEADER_SEQUENCE_URI = "UR" +SAM_HEADER_READGROUP_TAG = "RG" +SAM_HEADER_READGROUP_ID = "ID" +SAM_HEADER_READGROUP_BARCODE = "BC" +SAM_HEADER_READGROUP_SEQ_CENTER = "SC" +SAM_HEADER_READGROUP_DESCRIPTION = "DS" +SAM_HEADER_READGROUP_DATE = "DT" +SAM_HEADER_READGROUP_FLOWORDER = "FO" +SAM_HEADER_READGROUP_KEY_SEQUENCE = "KS" +SAM_HEADER_READGROUP_LIBRARY = "LB" +SAM_HEADER_READGROUP_PROGRAMS = "PG" +SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE = "PI" +SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY = "PL" +SAM_HEADER_READGROUP_PLATFORM_MODEL = "PM" +SAM_HEADER_READGROUP_PLATFORM_UNIT = "PU" +SAM_HEADER_READGROUP_SAMPLE = "SM" +SAM_FLAG_MULTIPLE = 1 +SAM_FLAG_ALL_PROPERLY_ALIGNED = 2 +SAM_FLAG_PROPERLY_PAIRED = 2 +SAM_FLAG_SEGMENT_UNMAPPED = 4 +SAM_FLAG_NEXT_SEGMENT_UNMAPPED = 8 +SAM_FLAG_MATE_UNMAPPED = 8 +SAM_FLAG_CURRENT_REVERSE_STRAND = 16 +SAM_FLAG_NEXT_REVERSE_STRAND = 32 +SAM_FLAG_MATE_REVERSE_STRAND = 32 +SAM_FLAG_FIRST_SEGMENT = 64 +SAM_FLAG_READ1 = 64 +SAM_FLAG_LAST_SEGMENT = 128 +SAM_FLAG_READ2 = 128 +SAM_FLAG_SECONDARY_ALIGNMENT = 256 +SAM_FLAG_NOT_PASSING_FILTERS = 512 +SAM_FLAG_DUPLICATE = 1024 +SAM_FLAG_SUPPLEMENTARY_ALIGNMENT = 2048 + +# enums +class SAM_HEADER_SORT_ORDER_TYPE(Enum): + unknown = 0 + coordinate = 1 + queryname = 2 + strand = 3 + +class SAM_HEADER_SUBSORT(Enum): + lexicographical = 0 + natural = 1 + umi = 2 + +class SAM_HEADER_RG_PLATFORM(Enum): + CAPILLARY = 0 + DNBSEQ = 1 + ELEMENT = 2 + HELICOS = 3 + ILLUMINA = 4 + IONTORRENT = 5 + LS454 = 6 + ONT = 7 + PACBIO = 8 + SINGULAR = 9 + SOLID = 10 + ULTIMA = 11 + diff --git a/constants/autogenerated/python/SamTags.py b/constants/autogenerated/python/SamTags.py new file mode 100644 index 00000000..7934af20 --- /dev/null +++ b/constants/autogenerated/python/SamTags.py @@ -0,0 +1,69 @@ +# autogenerated by reconstant - do not edit! +from enum import Enum + +# constants +SAM_TAG_AM = "AM" +SAM_TAG_AS = "AS" +SAM_TAG_BC = "BC" +SAM_TAG_BQ = "BQ" +SAM_TAG_BZ = "BZ" +SAM_TAG_CB = "CB" +SAM_TAG_CC = "CC" +SAM_TAG_CG = "CG" +SAM_TAG_CM = "CM" +SAM_TAG_CO = "CO" +SAM_TAG_CP = "CP" +SAM_TAG_CQ = "CQ" +SAM_TAG_CR = "CR" +SAM_TAG_CS = "CS" +SAM_TAG_CT = "CT" +SAM_TAG_CY = "CY" +SAM_TAG_E2 = "E2" +SAM_TAG_FI = "FI" +SAM_TAG_FS = "FS" +SAM_TAG_FZ = "FZ" +SAM_TAG_GC = "GC" +SAM_TAG_GQ = "GQ" +SAM_TAG_GS = "GS" +SAM_TAG_H0 = "H0" +SAM_TAG_H1 = "H1" +SAM_TAG_H2 = "H2" +SAM_TAG_HI = "HI" +SAM_TAG_IH = "IH" +SAM_TAG_LB = "LB" +SAM_TAG_MC = "MC" +SAM_TAG_MD = "MD" +SAM_TAG_MF = "MF" +SAM_TAG_MI = "MI" +SAM_TAG_ML = "ML" +SAM_TAG_MM = "MM" +SAM_TAG_MN = "MN" +SAM_TAG_MQ = "MQ" +SAM_TAG_NH = "NH" +SAM_TAG_NM = "NM" +SAM_TAG_OA = "OA" +SAM_TAG_OC = "OC" +SAM_TAG_OP = "OP" +SAM_TAG_OQ = "OQ" +SAM_TAG_OX = "OX" +SAM_TAG_PG = "PG" +SAM_TAG_PQ = "PQ" +SAM_TAG_PT = "PT" +SAM_TAG_PU = "PU" +SAM_TAG_Q2 = "Q2" +SAM_TAG_QT = "QT" +SAM_TAG_QX = "QX" +SAM_TAG_R2 = "R2" +SAM_TAG_RG = "RG" +SAM_TAG_RT = "RT" +SAM_TAG_RX = "RX" +SAM_TAG_S2 = "S2" +SAM_TAG_SA = "SA" +SAM_TAG_SM = "SM" +SAM_TAG_SQ = "SQ" +SAM_TAG_TC = "TC" +SAM_TAG_TS = "TS" +SAM_TAG_U2 = "U2" +SAM_TAG_UQ = "UQ" + +# enums diff --git a/constants/autogenerated/rust/BAM.rs b/constants/autogenerated/rust/BAM.rs new file mode 100644 index 00000000..61ff608f --- /dev/null +++ b/constants/autogenerated/rust/BAM.rs @@ -0,0 +1,6 @@ +// autogenerated by reconstant - do not edit! + +// constants +pub const MAGIC: &str = "BAM\\1"; + +// enums diff --git a/constants/autogenerated/rust/SAM.rs b/constants/autogenerated/rust/SAM.rs new file mode 100644 index 00000000..19691686 --- /dev/null +++ b/constants/autogenerated/rust/SAM.rs @@ -0,0 +1,77 @@ +// autogenerated by reconstant - do not edit! + +// constants +pub const SAM_HEADER_TAG: &str = "HD"; +pub const SAM_HEADER_VERSION_TAG: &str = "VN"; +pub const SAM_HEADER_SORTORDER_TAG: &str = "SO"; +pub const SAM_HEADER_GROUPORDER_TAG: &str = "GO"; +pub const SAM_HEADER_SUBSORT_TAG: &str = "SS"; +pub const SAM_HEADER_REFERENCE_SEQUENCE: &str = "SQ"; +pub const SAM_HEADER_SEQUENCE_LENGTH: &str = "LN"; +pub const SAM_HEADER_SEQUENCE_ALTERNATIVE: &str = "AH"; +pub const SAM_HEADER_SEQUENCE_ALTERNATIVE_NAME: &str = "AN"; +pub const SAM_HEADER_SEQUENCE_ASSEMBLY_ID: &str = "AS"; +pub const SAM_HEADER_SEQUENCE_DESCRIPTION: &str = "DS"; +pub const SAM_HEADER_SEQUENCE_MD5: &str = "M5"; +pub const SAM_HEADER_SEQUENCE_SPECIES: &str = "SP"; +pub const SAM_HEADER_SEQUENCE_TOPOLOGY: &str = "TP"; +pub const SAM_HEADER_SEQUENCE_URI: &str = "UR"; +pub const SAM_HEADER_READGROUP_TAG: &str = "RG"; +pub const SAM_HEADER_READGROUP_ID: &str = "ID"; +pub const SAM_HEADER_READGROUP_BARCODE: &str = "BC"; +pub const SAM_HEADER_READGROUP_SEQ_CENTER: &str = "SC"; +pub const SAM_HEADER_READGROUP_DESCRIPTION: &str = "DS"; +pub const SAM_HEADER_READGROUP_DATE: &str = "DT"; +pub const SAM_HEADER_READGROUP_FLOWORDER: &str = "FO"; +pub const SAM_HEADER_READGROUP_KEY_SEQUENCE: &str = "KS"; +pub const SAM_HEADER_READGROUP_LIBRARY: &str = "LB"; +pub const SAM_HEADER_READGROUP_PROGRAMS: &str = "PG"; +pub const SAM_HEADER_READGROUP_PREDICTED_INSERTSIZE: &str = "PI"; +pub const SAM_HEADER_READGROUP_PLATFORM_TECHNOLOGY: &str = "PL"; +pub const SAM_HEADER_READGROUP_PLATFORM_MODEL: &str = "PM"; +pub const SAM_HEADER_READGROUP_PLATFORM_UNIT: &str = "PU"; +pub const SAM_HEADER_READGROUP_SAMPLE: &str = "SM"; +pub const SAM_FLAG_MULTIPLE: i32 = 1; +pub const SAM_FLAG_ALL_PROPERLY_ALIGNED: i32 = 2; +pub const SAM_FLAG_PROPERLY_PAIRED: i32 = 2; +pub const SAM_FLAG_SEGMENT_UNMAPPED: i32 = 4; +pub const SAM_FLAG_NEXT_SEGMENT_UNMAPPED: i32 = 8; +pub const SAM_FLAG_MATE_UNMAPPED: i32 = 8; +pub const SAM_FLAG_CURRENT_REVERSE_STRAND: i32 = 16; +pub const SAM_FLAG_NEXT_REVERSE_STRAND: i32 = 32; +pub const SAM_FLAG_MATE_REVERSE_STRAND: i32 = 32; +pub const SAM_FLAG_FIRST_SEGMENT: i32 = 64; +pub const SAM_FLAG_READ1: i32 = 64; +pub const SAM_FLAG_LAST_SEGMENT: i32 = 128; +pub const SAM_FLAG_READ2: i32 = 128; +pub const SAM_FLAG_SECONDARY_ALIGNMENT: i32 = 256; +pub const SAM_FLAG_NOT_PASSING_FILTERS: i32 = 512; +pub const SAM_FLAG_DUPLICATE: i32 = 1024; +pub const SAM_FLAG_SUPPLEMENTARY_ALIGNMENT: i32 = 2048; + +// enums +pub enum SAM_HEADER_SORT_ORDER_TYPE { + unknown, + coordinate, + queryname, + strand +} +pub enum SAM_HEADER_SUBSORT { + lexicographical, + natural, + umi +} +pub enum SAM_HEADER_RG_PLATFORM { + CAPILLARY, + DNBSEQ, + ELEMENT, + HELICOS, + ILLUMINA, + IONTORRENT, + LS454, + ONT, + PACBIO, + SINGULAR, + SOLID, + ULTIMA +} diff --git a/constants/autogenerated/rust/SamTags.rs b/constants/autogenerated/rust/SamTags.rs new file mode 100644 index 00000000..d978993b --- /dev/null +++ b/constants/autogenerated/rust/SamTags.rs @@ -0,0 +1,68 @@ +// autogenerated by reconstant - do not edit! + +// constants +pub const SAM_TAG_AM: &str = "AM"; +pub const SAM_TAG_AS: &str = "AS"; +pub const SAM_TAG_BC: &str = "BC"; +pub const SAM_TAG_BQ: &str = "BQ"; +pub const SAM_TAG_BZ: &str = "BZ"; +pub const SAM_TAG_CB: &str = "CB"; +pub const SAM_TAG_CC: &str = "CC"; +pub const SAM_TAG_CG: &str = "CG"; +pub const SAM_TAG_CM: &str = "CM"; +pub const SAM_TAG_CO: &str = "CO"; +pub const SAM_TAG_CP: &str = "CP"; +pub const SAM_TAG_CQ: &str = "CQ"; +pub const SAM_TAG_CR: &str = "CR"; +pub const SAM_TAG_CS: &str = "CS"; +pub const SAM_TAG_CT: &str = "CT"; +pub const SAM_TAG_CY: &str = "CY"; +pub const SAM_TAG_E2: &str = "E2"; +pub const SAM_TAG_FI: &str = "FI"; +pub const SAM_TAG_FS: &str = "FS"; +pub const SAM_TAG_FZ: &str = "FZ"; +pub const SAM_TAG_GC: &str = "GC"; +pub const SAM_TAG_GQ: &str = "GQ"; +pub const SAM_TAG_GS: &str = "GS"; +pub const SAM_TAG_H0: &str = "H0"; +pub const SAM_TAG_H1: &str = "H1"; +pub const SAM_TAG_H2: &str = "H2"; +pub const SAM_TAG_HI: &str = "HI"; +pub const SAM_TAG_IH: &str = "IH"; +pub const SAM_TAG_LB: &str = "LB"; +pub const SAM_TAG_MC: &str = "MC"; +pub const SAM_TAG_MD: &str = "MD"; +pub const SAM_TAG_MF: &str = "MF"; +pub const SAM_TAG_MI: &str = "MI"; +pub const SAM_TAG_ML: &str = "ML"; +pub const SAM_TAG_MM: &str = "MM"; +pub const SAM_TAG_MN: &str = "MN"; +pub const SAM_TAG_MQ: &str = "MQ"; +pub const SAM_TAG_NH: &str = "NH"; +pub const SAM_TAG_NM: &str = "NM"; +pub const SAM_TAG_OA: &str = "OA"; +pub const SAM_TAG_OC: &str = "OC"; +pub const SAM_TAG_OP: &str = "OP"; +pub const SAM_TAG_OQ: &str = "OQ"; +pub const SAM_TAG_OX: &str = "OX"; +pub const SAM_TAG_PG: &str = "PG"; +pub const SAM_TAG_PQ: &str = "PQ"; +pub const SAM_TAG_PT: &str = "PT"; +pub const SAM_TAG_PU: &str = "PU"; +pub const SAM_TAG_Q2: &str = "Q2"; +pub const SAM_TAG_QT: &str = "QT"; +pub const SAM_TAG_QX: &str = "QX"; +pub const SAM_TAG_R2: &str = "R2"; +pub const SAM_TAG_RG: &str = "RG"; +pub const SAM_TAG_RT: &str = "RT"; +pub const SAM_TAG_RX: &str = "RX"; +pub const SAM_TAG_S2: &str = "S2"; +pub const SAM_TAG_SA: &str = "SA"; +pub const SAM_TAG_SM: &str = "SM"; +pub const SAM_TAG_SQ: &str = "SQ"; +pub const SAM_TAG_TC: &str = "TC"; +pub const SAM_TAG_TS: &str = "TS"; +pub const SAM_TAG_U2: &str = "U2"; +pub const SAM_TAG_UQ: &str = "UQ"; + +// enums