/* encodeDataWarehouse.h was originally generated by the autoSql program, which also * generated encodeDataWarehouse.c and encodeDataWarehouse.sql. This header links the database and * the RAM representation of objects. */ /* Copyright (C) 2014 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef ENCODEDATAWAREHOUSE_H #define ENCODEDATAWAREHOUSE_H #include "jksql.h" #define EDWSETTINGS_NUM_COLS 3 extern char *edwSettingsCommaSepFieldNames; struct edwSettings /* Settings used to configure warehouse */ { struct edwSettings *next; /* Next in singly linked list. */ unsigned id; /* Settings ID */ char *name; /* Settings name, can't be reused */ char *val; /* Settings value, some undefined but not huge thing */ }; void edwSettingsStaticLoad(char **row, struct edwSettings *ret); /* Load a row from edwSettings table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwSettings *edwSettingsLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwSettings from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwSettingsFreeList(). */ void edwSettingsSaveToDb(struct sqlConnection *conn, struct edwSettings *el, char *tableName, int updateSize); /* Save edwSettings as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwSettings *edwSettingsLoad(char **row); /* Load a edwSettings from row fetched with select * from edwSettings * from database. Dispose of this with edwSettingsFree(). */ struct edwSettings *edwSettingsLoadAll(char *fileName); /* Load all edwSettings from whitespace-separated file. * Dispose of this with edwSettingsFreeList(). */ struct edwSettings *edwSettingsLoadAllByChar(char *fileName, char chopper); /* Load all edwSettings from chopper separated file. * Dispose of this with edwSettingsFreeList(). */ #define edwSettingsLoadAllByTab(a) edwSettingsLoadAllByChar(a, '\t'); /* Load all edwSettings from tab separated file. * Dispose of this with edwSettingsFreeList(). */ struct edwSettings *edwSettingsCommaIn(char **pS, struct edwSettings *ret); /* Create a edwSettings out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwSettings */ void edwSettingsFree(struct edwSettings **pEl); /* Free a single dynamically allocated edwSettings such as created * with edwSettingsLoad(). */ void edwSettingsFreeList(struct edwSettings **pList); /* Free a list of dynamically allocated edwSettings's */ void edwSettingsOutput(struct edwSettings *el, FILE *f, char sep, char lastSep); /* Print out edwSettings. Separate fields with sep. Follow last field with lastSep. */ #define edwSettingsTabOut(el,f) edwSettingsOutput(el,f,'\t','\n'); /* Print out edwSettings as a line in a tab-separated file. */ #define edwSettingsCommaOut(el,f) edwSettingsOutput(el,f,',',','); /* Print out edwSettings as a comma separated list including final comma. */ #define EDWUSER_NUM_COLS 4 extern char *edwUserCommaSepFieldNames; struct edwUser /* Someone who submits files to or otherwise interacts with big data warehouse */ { struct edwUser *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented user ID */ char *email; /* Email address - required */ char uuid[38]; /* Help to synchronize us with Stanford. */ signed char isAdmin; /* If true the use can modify other people's files too. */ }; void edwUserStaticLoad(char **row, struct edwUser *ret); /* Load a row from edwUser table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwUser *edwUserLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwUser from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwUserFreeList(). */ void edwUserSaveToDb(struct sqlConnection *conn, struct edwUser *el, char *tableName, int updateSize); /* Save edwUser as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwUser *edwUserLoad(char **row); /* Load a edwUser from row fetched with select * from edwUser * from database. Dispose of this with edwUserFree(). */ struct edwUser *edwUserLoadAll(char *fileName); /* Load all edwUser from whitespace-separated file. * Dispose of this with edwUserFreeList(). */ struct edwUser *edwUserLoadAllByChar(char *fileName, char chopper); /* Load all edwUser from chopper separated file. * Dispose of this with edwUserFreeList(). */ #define edwUserLoadAllByTab(a) edwUserLoadAllByChar(a, '\t'); /* Load all edwUser from tab separated file. * Dispose of this with edwUserFreeList(). */ struct edwUser *edwUserCommaIn(char **pS, struct edwUser *ret); /* Create a edwUser out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwUser */ void edwUserFree(struct edwUser **pEl); /* Free a single dynamically allocated edwUser such as created * with edwUserLoad(). */ void edwUserFreeList(struct edwUser **pList); /* Free a list of dynamically allocated edwUser's */ void edwUserOutput(struct edwUser *el, FILE *f, char sep, char lastSep); /* Print out edwUser. Separate fields with sep. Follow last field with lastSep. */ #define edwUserTabOut(el,f) edwUserOutput(el,f,'\t','\n'); /* Print out edwUser as a line in a tab-separated file. */ #define edwUserCommaOut(el,f) edwUserOutput(el,f,',',','); /* Print out edwUser as a comma separated list including final comma. */ #define EDWSCRIPTREGISTRY_NUM_COLS 6 extern char *edwScriptRegistryCommaSepFieldNames; struct edwScriptRegistry /* A script that is authorized to submit on behalf of a user */ { struct edwScriptRegistry *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented script ID */ unsigned userId; /* Associated user */ char *name; /* Script name - unique in system and autogenerated */ char *description; /* Script description */ char *secretHash; /* Hashed script password */ int submitCount; /* Number of submissions attempted */ }; void edwScriptRegistryStaticLoad(char **row, struct edwScriptRegistry *ret); /* Load a row from edwScriptRegistry table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwScriptRegistry *edwScriptRegistryLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwScriptRegistry from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwScriptRegistryFreeList(). */ void edwScriptRegistrySaveToDb(struct sqlConnection *conn, struct edwScriptRegistry *el, char *tableName, int updateSize); /* Save edwScriptRegistry as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwScriptRegistry *edwScriptRegistryLoad(char **row); /* Load a edwScriptRegistry from row fetched with select * from edwScriptRegistry * from database. Dispose of this with edwScriptRegistryFree(). */ struct edwScriptRegistry *edwScriptRegistryLoadAll(char *fileName); /* Load all edwScriptRegistry from whitespace-separated file. * Dispose of this with edwScriptRegistryFreeList(). */ struct edwScriptRegistry *edwScriptRegistryLoadAllByChar(char *fileName, char chopper); /* Load all edwScriptRegistry from chopper separated file. * Dispose of this with edwScriptRegistryFreeList(). */ #define edwScriptRegistryLoadAllByTab(a) edwScriptRegistryLoadAllByChar(a, '\t'); /* Load all edwScriptRegistry from tab separated file. * Dispose of this with edwScriptRegistryFreeList(). */ struct edwScriptRegistry *edwScriptRegistryCommaIn(char **pS, struct edwScriptRegistry *ret); /* Create a edwScriptRegistry out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwScriptRegistry */ void edwScriptRegistryFree(struct edwScriptRegistry **pEl); /* Free a single dynamically allocated edwScriptRegistry such as created * with edwScriptRegistryLoad(). */ void edwScriptRegistryFreeList(struct edwScriptRegistry **pList); /* Free a list of dynamically allocated edwScriptRegistry's */ void edwScriptRegistryOutput(struct edwScriptRegistry *el, FILE *f, char sep, char lastSep); /* Print out edwScriptRegistry. Separate fields with sep. Follow last field with lastSep. */ #define edwScriptRegistryTabOut(el,f) edwScriptRegistryOutput(el,f,'\t','\n'); /* Print out edwScriptRegistry as a line in a tab-separated file. */ #define edwScriptRegistryCommaOut(el,f) edwScriptRegistryOutput(el,f,',',','); /* Print out edwScriptRegistry as a comma separated list including final comma. */ #define EDWHOST_NUM_COLS 10 extern char *edwHostCommaSepFieldNames; struct edwHost /* A web host we have collected files from - something like www.ncbi.nlm.gov or google.com */ { struct edwHost *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented host id */ char *name; /* Name (before DNS lookup) */ long long lastOkTime; /* Last time host was ok in seconds since 1970 */ long long lastNotOkTime; /* Last time host was not ok in seconds since 1970 */ long long firstAdded; /* Time host was first seen */ char *errorMessage; /* If non-empty contains last error message from host. If empty host is ok */ long long openSuccesses; /* Number of times files have been opened ok from this host */ long long openFails; /* Number of times files have failed to open from this host */ long long historyBits; /* Open history with most recent in least significant bit. 0 for connection failed, 1 for success */ int paraFetchStreams; /* Number of open streams for paraFetch command. 10 for most places, 30 for Barcelona */ }; void edwHostStaticLoad(char **row, struct edwHost *ret); /* Load a row from edwHost table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwHost *edwHostLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwHost from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwHostFreeList(). */ void edwHostSaveToDb(struct sqlConnection *conn, struct edwHost *el, char *tableName, int updateSize); /* Save edwHost as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwHost *edwHostLoad(char **row); /* Load a edwHost from row fetched with select * from edwHost * from database. Dispose of this with edwHostFree(). */ struct edwHost *edwHostLoadAll(char *fileName); /* Load all edwHost from whitespace-separated file. * Dispose of this with edwHostFreeList(). */ struct edwHost *edwHostLoadAllByChar(char *fileName, char chopper); /* Load all edwHost from chopper separated file. * Dispose of this with edwHostFreeList(). */ #define edwHostLoadAllByTab(a) edwHostLoadAllByChar(a, '\t'); /* Load all edwHost from tab separated file. * Dispose of this with edwHostFreeList(). */ struct edwHost *edwHostCommaIn(char **pS, struct edwHost *ret); /* Create a edwHost out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwHost */ void edwHostFree(struct edwHost **pEl); /* Free a single dynamically allocated edwHost such as created * with edwHostLoad(). */ void edwHostFreeList(struct edwHost **pList); /* Free a list of dynamically allocated edwHost's */ void edwHostOutput(struct edwHost *el, FILE *f, char sep, char lastSep); /* Print out edwHost. Separate fields with sep. Follow last field with lastSep. */ #define edwHostTabOut(el,f) edwHostOutput(el,f,'\t','\n'); /* Print out edwHost as a line in a tab-separated file. */ #define edwHostCommaOut(el,f) edwHostOutput(el,f,',',','); /* Print out edwHost as a comma separated list including final comma. */ #define EDWSUBMITDIR_NUM_COLS 10 extern char *edwSubmitDirCommaSepFieldNames; struct edwSubmitDir /* An external data directory we have collected a submit from */ { struct edwSubmitDir *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented id */ char *url; /* Web-mounted directory. Includes protocol, host, and final '/' */ unsigned hostId; /* Id of host it's on */ long long lastOkTime; /* Last time submit dir was ok in seconds since 1970 */ long long lastNotOkTime; /* Last time submit dir was not ok in seconds since 1970 */ long long firstAdded; /* Time submit dir was first seen */ char *errorMessage; /* If non-empty contains last error message from dir. If empty dir is ok */ long long openSuccesses; /* Number of times files have been opened ok from this dir */ long long openFails; /* Number of times files have failed to open from this dir */ long long historyBits; /* Open history with most recent in least significant bit. 0 for upload failed, 1 for success */ }; void edwSubmitDirStaticLoad(char **row, struct edwSubmitDir *ret); /* Load a row from edwSubmitDir table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwSubmitDir *edwSubmitDirLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwSubmitDir from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwSubmitDirFreeList(). */ void edwSubmitDirSaveToDb(struct sqlConnection *conn, struct edwSubmitDir *el, char *tableName, int updateSize); /* Save edwSubmitDir as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwSubmitDir *edwSubmitDirLoad(char **row); /* Load a edwSubmitDir from row fetched with select * from edwSubmitDir * from database. Dispose of this with edwSubmitDirFree(). */ struct edwSubmitDir *edwSubmitDirLoadAll(char *fileName); /* Load all edwSubmitDir from whitespace-separated file. * Dispose of this with edwSubmitDirFreeList(). */ struct edwSubmitDir *edwSubmitDirLoadAllByChar(char *fileName, char chopper); /* Load all edwSubmitDir from chopper separated file. * Dispose of this with edwSubmitDirFreeList(). */ #define edwSubmitDirLoadAllByTab(a) edwSubmitDirLoadAllByChar(a, '\t'); /* Load all edwSubmitDir from tab separated file. * Dispose of this with edwSubmitDirFreeList(). */ struct edwSubmitDir *edwSubmitDirCommaIn(char **pS, struct edwSubmitDir *ret); /* Create a edwSubmitDir out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwSubmitDir */ void edwSubmitDirFree(struct edwSubmitDir **pEl); /* Free a single dynamically allocated edwSubmitDir such as created * with edwSubmitDirLoad(). */ void edwSubmitDirFreeList(struct edwSubmitDir **pList); /* Free a list of dynamically allocated edwSubmitDir's */ void edwSubmitDirOutput(struct edwSubmitDir *el, FILE *f, char sep, char lastSep); /* Print out edwSubmitDir. Separate fields with sep. Follow last field with lastSep. */ #define edwSubmitDirTabOut(el,f) edwSubmitDirOutput(el,f,'\t','\n'); /* Print out edwSubmitDir as a line in a tab-separated file. */ #define edwSubmitDirCommaOut(el,f) edwSubmitDirOutput(el,f,',',','); /* Print out edwSubmitDir as a comma separated list including final comma. */ #define EDWFILE_NUM_COLS 14 extern char *edwFileCommaSepFieldNames; struct edwFile /* A file we are tracking that we intend to and maybe have uploaded */ { struct edwFile *next; /* Next in singly linked list. */ unsigned id; /* Autoincrementing file id */ unsigned submitId; /* Links to id in submit table */ unsigned submitDirId; /* Links to id in submitDir table */ char *submitFileName; /* File name in submit relative to submit dir */ char *edwFileName; /* File name in big data warehouse relative to edw root dir */ long long startUploadTime; /* Time when upload started - 0 if not started */ long long endUploadTime; /* Time when upload finished - 0 if not finished */ long long updateTime; /* Update time (on system it was uploaded from) */ long long size; /* File size in manifest */ char md5[33]; /* md5 sum of file contents */ char *tags; /* CGI encoded name=val pairs from manifest */ char *errorMessage; /* If non-empty contains last error message from upload. If empty upload is ok */ char *deprecated; /* If non-empty why you shouldn't use this file any more. */ unsigned replacedBy; /* If non-zero id of file that replaces this one. */ }; void edwFileStaticLoad(char **row, struct edwFile *ret); /* Load a row from edwFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwFile *edwFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwFile from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwFileFreeList(). */ void edwFileSaveToDb(struct sqlConnection *conn, struct edwFile *el, char *tableName, int updateSize); /* Save edwFile as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwFile *edwFileLoad(char **row); /* Load a edwFile from row fetched with select * from edwFile * from database. Dispose of this with edwFileFree(). */ struct edwFile *edwFileLoadAll(char *fileName); /* Load all edwFile from whitespace-separated file. * Dispose of this with edwFileFreeList(). */ struct edwFile *edwFileLoadAllByChar(char *fileName, char chopper); /* Load all edwFile from chopper separated file. * Dispose of this with edwFileFreeList(). */ #define edwFileLoadAllByTab(a) edwFileLoadAllByChar(a, '\t'); /* Load all edwFile from tab separated file. * Dispose of this with edwFileFreeList(). */ struct edwFile *edwFileCommaIn(char **pS, struct edwFile *ret); /* Create a edwFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwFile */ void edwFileFree(struct edwFile **pEl); /* Free a single dynamically allocated edwFile such as created * with edwFileLoad(). */ void edwFileFreeList(struct edwFile **pList); /* Free a list of dynamically allocated edwFile's */ void edwFileOutput(struct edwFile *el, FILE *f, char sep, char lastSep); /* Print out edwFile. Separate fields with sep. Follow last field with lastSep. */ #define edwFileTabOut(el,f) edwFileOutput(el,f,'\t','\n'); /* Print out edwFile as a line in a tab-separated file. */ #define edwFileCommaOut(el,f) edwFileOutput(el,f,',',','); /* Print out edwFile as a comma separated list including final comma. */ #define EDWSUBMIT_NUM_COLS 16 extern char *edwSubmitCommaSepFieldNames; struct edwSubmit /* A data submit, typically containing many files. Always associated with a submit dir. */ { struct edwSubmit *next; /* Next in singly linked list. */ unsigned id; /* Autoincremented submit id */ char *url; /* Url to validated.txt format file. We copy this file over and give it a fileId if we can. */ long long startUploadTime; /* Time at start of submit */ long long endUploadTime; /* Time at end of upload - 0 if not finished */ unsigned userId; /* Connects to user table id field */ unsigned submitFileId; /* Points to validated.txt file for submit. */ unsigned submitDirId; /* Points to the submitDir */ unsigned fileCount; /* Number of files that will be in submit if it were complete. */ unsigned oldFiles; /* Number of files in submission that were already in warehouse. */ unsigned newFiles; /* Number of files in submission that are newly uploaded. */ long long byteCount; /* Total bytes in submission including old and new */ long long oldBytes; /* Bytes in old files. */ long long newBytes; /* Bytes in new files (so far). */ char *errorMessage; /* If non-empty contains last error message. If empty submit is ok */ unsigned fileIdInTransit; /* edwFile.id of file currently being transferred or zero */ unsigned metaChangeCount; /* Number of files where metadata changed by submission */ }; void edwSubmitStaticLoad(char **row, struct edwSubmit *ret); /* Load a row from edwSubmit table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwSubmit *edwSubmitLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwSubmit from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwSubmitFreeList(). */ void edwSubmitSaveToDb(struct sqlConnection *conn, struct edwSubmit *el, char *tableName, int updateSize); /* Save edwSubmit as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwSubmit *edwSubmitLoad(char **row); /* Load a edwSubmit from row fetched with select * from edwSubmit * from database. Dispose of this with edwSubmitFree(). */ struct edwSubmit *edwSubmitLoadAll(char *fileName); /* Load all edwSubmit from whitespace-separated file. * Dispose of this with edwSubmitFreeList(). */ struct edwSubmit *edwSubmitLoadAllByChar(char *fileName, char chopper); /* Load all edwSubmit from chopper separated file. * Dispose of this with edwSubmitFreeList(). */ #define edwSubmitLoadAllByTab(a) edwSubmitLoadAllByChar(a, '\t'); /* Load all edwSubmit from tab separated file. * Dispose of this with edwSubmitFreeList(). */ struct edwSubmit *edwSubmitCommaIn(char **pS, struct edwSubmit *ret); /* Create a edwSubmit out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwSubmit */ void edwSubmitFree(struct edwSubmit **pEl); /* Free a single dynamically allocated edwSubmit such as created * with edwSubmitLoad(). */ void edwSubmitFreeList(struct edwSubmit **pList); /* Free a list of dynamically allocated edwSubmit's */ void edwSubmitOutput(struct edwSubmit *el, FILE *f, char sep, char lastSep); /* Print out edwSubmit. Separate fields with sep. Follow last field with lastSep. */ #define edwSubmitTabOut(el,f) edwSubmitOutput(el,f,'\t','\n'); /* Print out edwSubmit as a line in a tab-separated file. */ #define edwSubmitCommaOut(el,f) edwSubmitOutput(el,f,',',','); /* Print out edwSubmit as a comma separated list including final comma. */ #define EDWSUBSCRIBER_NUM_COLS 7 extern char *edwSubscriberCommaSepFieldNames; struct edwSubscriber /* Subscribers can have programs that are called at various points during data submission */ { struct edwSubscriber *next; /* Next in singly linked list. */ unsigned id; /* ID of subscriber */ char *name; /* Name of subscriber */ double runOrder; /* Determines order subscribers run in. In case of tie lowest id wins. */ char *filePattern; /* A string with * and ? wildcards to match files we care about */ char *dirPattern; /* A string with * and ? wildcards to match hub dir URLs we care about */ char *tagPattern; /* A cgi-encoded string of tag=wildcard pairs. */ char *onFileEndUpload; /* A unix command string to run with a %u where file id goes */ }; void edwSubscriberStaticLoad(char **row, struct edwSubscriber *ret); /* Load a row from edwSubscriber table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwSubscriber *edwSubscriberLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwSubscriber from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwSubscriberFreeList(). */ void edwSubscriberSaveToDb(struct sqlConnection *conn, struct edwSubscriber *el, char *tableName, int updateSize); /* Save edwSubscriber as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwSubscriber *edwSubscriberLoad(char **row); /* Load a edwSubscriber from row fetched with select * from edwSubscriber * from database. Dispose of this with edwSubscriberFree(). */ struct edwSubscriber *edwSubscriberLoadAll(char *fileName); /* Load all edwSubscriber from whitespace-separated file. * Dispose of this with edwSubscriberFreeList(). */ struct edwSubscriber *edwSubscriberLoadAllByChar(char *fileName, char chopper); /* Load all edwSubscriber from chopper separated file. * Dispose of this with edwSubscriberFreeList(). */ #define edwSubscriberLoadAllByTab(a) edwSubscriberLoadAllByChar(a, '\t'); /* Load all edwSubscriber from tab separated file. * Dispose of this with edwSubscriberFreeList(). */ struct edwSubscriber *edwSubscriberCommaIn(char **pS, struct edwSubscriber *ret); /* Create a edwSubscriber out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwSubscriber */ void edwSubscriberFree(struct edwSubscriber **pEl); /* Free a single dynamically allocated edwSubscriber such as created * with edwSubscriberLoad(). */ void edwSubscriberFreeList(struct edwSubscriber **pList); /* Free a list of dynamically allocated edwSubscriber's */ void edwSubscriberOutput(struct edwSubscriber *el, FILE *f, char sep, char lastSep); /* Print out edwSubscriber. Separate fields with sep. Follow last field with lastSep. */ #define edwSubscriberTabOut(el,f) edwSubscriberOutput(el,f,'\t','\n'); /* Print out edwSubscriber as a line in a tab-separated file. */ #define edwSubscriberCommaOut(el,f) edwSubscriberOutput(el,f,',',','); /* Print out edwSubscriber as a comma separated list including final comma. */ #define EDWASSEMBLY_NUM_COLS 8 extern char *edwAssemblyCommaSepFieldNames; struct edwAssembly /* An assembly - includes reference to a two bit file, and a little name and summary info. */ { struct edwAssembly *next; /* Next in singly linked list. */ unsigned id; /* Assembly ID */ unsigned taxon; /* NCBI taxon number */ char *name; /* Some human readable name to distinguish this from other collections of DNA */ char *ucscDb; /* Which UCSC database (mm9? hg19?) associated with it. */ unsigned twoBitId; /* File ID of associated twoBit file */ long long baseCount; /* Count of bases including N's */ long long realBaseCount; /* Count of non-N bases in assembly */ unsigned seqCount; /* Number of chromosomes or other distinct sequences in assembly */ }; void edwAssemblyStaticLoad(char **row, struct edwAssembly *ret); /* Load a row from edwAssembly table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwAssembly *edwAssemblyLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwAssembly from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwAssemblyFreeList(). */ void edwAssemblySaveToDb(struct sqlConnection *conn, struct edwAssembly *el, char *tableName, int updateSize); /* Save edwAssembly as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwAssembly *edwAssemblyLoad(char **row); /* Load a edwAssembly from row fetched with select * from edwAssembly * from database. Dispose of this with edwAssemblyFree(). */ struct edwAssembly *edwAssemblyLoadAll(char *fileName); /* Load all edwAssembly from whitespace-separated file. * Dispose of this with edwAssemblyFreeList(). */ struct edwAssembly *edwAssemblyLoadAllByChar(char *fileName, char chopper); /* Load all edwAssembly from chopper separated file. * Dispose of this with edwAssemblyFreeList(). */ #define edwAssemblyLoadAllByTab(a) edwAssemblyLoadAllByChar(a, '\t'); /* Load all edwAssembly from tab separated file. * Dispose of this with edwAssemblyFreeList(). */ struct edwAssembly *edwAssemblyCommaIn(char **pS, struct edwAssembly *ret); /* Create a edwAssembly out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwAssembly */ void edwAssemblyFree(struct edwAssembly **pEl); /* Free a single dynamically allocated edwAssembly such as created * with edwAssemblyLoad(). */ void edwAssemblyFreeList(struct edwAssembly **pList); /* Free a list of dynamically allocated edwAssembly's */ void edwAssemblyOutput(struct edwAssembly *el, FILE *f, char sep, char lastSep); /* Print out edwAssembly. Separate fields with sep. Follow last field with lastSep. */ #define edwAssemblyTabOut(el,f) edwAssemblyOutput(el,f,'\t','\n'); /* Print out edwAssembly as a line in a tab-separated file. */ #define edwAssemblyCommaOut(el,f) edwAssemblyOutput(el,f,',',','); /* Print out edwAssembly as a comma separated list including final comma. */ #define EDWBIOSAMPLE_NUM_COLS 4 extern char *edwBiosampleCommaSepFieldNames; struct edwBiosample /* A biosample - not much info here, just enough to drive analysis pipeline */ { struct edwBiosample *next; /* Next in singly linked list. */ unsigned id; /* Biosample id */ char *term; /* Human readable. Shared with ENCODE2. */ unsigned taxon; /* NCBI taxon number - 9606 for human. */ char *sex; /* One letter code: M male, F female, B both, U unknown */ }; void edwBiosampleStaticLoad(char **row, struct edwBiosample *ret); /* Load a row from edwBiosample table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwBiosample *edwBiosampleLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwBiosample from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwBiosampleFreeList(). */ void edwBiosampleSaveToDb(struct sqlConnection *conn, struct edwBiosample *el, char *tableName, int updateSize); /* Save edwBiosample as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwBiosample *edwBiosampleLoad(char **row); /* Load a edwBiosample from row fetched with select * from edwBiosample * from database. Dispose of this with edwBiosampleFree(). */ struct edwBiosample *edwBiosampleLoadAll(char *fileName); /* Load all edwBiosample from whitespace-separated file. * Dispose of this with edwBiosampleFreeList(). */ struct edwBiosample *edwBiosampleLoadAllByChar(char *fileName, char chopper); /* Load all edwBiosample from chopper separated file. * Dispose of this with edwBiosampleFreeList(). */ #define edwBiosampleLoadAllByTab(a) edwBiosampleLoadAllByChar(a, '\t'); /* Load all edwBiosample from tab separated file. * Dispose of this with edwBiosampleFreeList(). */ struct edwBiosample *edwBiosampleCommaIn(char **pS, struct edwBiosample *ret); /* Create a edwBiosample out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwBiosample */ void edwBiosampleFree(struct edwBiosample **pEl); /* Free a single dynamically allocated edwBiosample such as created * with edwBiosampleLoad(). */ void edwBiosampleFreeList(struct edwBiosample **pList); /* Free a list of dynamically allocated edwBiosample's */ void edwBiosampleOutput(struct edwBiosample *el, FILE *f, char sep, char lastSep); /* Print out edwBiosample. Separate fields with sep. Follow last field with lastSep. */ #define edwBiosampleTabOut(el,f) edwBiosampleOutput(el,f,'\t','\n'); /* Print out edwBiosample as a line in a tab-separated file. */ #define edwBiosampleCommaOut(el,f) edwBiosampleOutput(el,f,',',','); /* Print out edwBiosample as a comma separated list including final comma. */ #define EDWEXPERIMENT_NUM_COLS 8 extern char *edwExperimentCommaSepFieldNames; struct edwExperiment /* An experiment - ideally will include a couple of biological replicates. Downloaded from Stanford. */ { struct edwExperiment *next; /* Next in singly linked list. */ char accession[17]; /* Something like ENCSR000CFA. ID shared with Stanford. */ char *dataType; /* Something liek RNA-seq, DNase-seq, ChIP-seq. Computed at UCSC. */ char *lab; /* Lab PI name and institution. Is lab.title at Stanford. */ char *biosample; /* Cell line name, tissue source, etc. Is biosample_term_name at Stanford. */ char *rfa; /* Something like 'ENCODE2' or 'ENCODE3'. Is award.rfa at Stanford. */ char *assayType; /* Similar to dataType. Is assay_term_name at Stanford. */ char *ipTarget; /* The target for the immunoprecipitation in ChIP & RIP. */ char *control; /* Primary control for experiment. Usually another experiment accession. */ }; void edwExperimentStaticLoad(char **row, struct edwExperiment *ret); /* Load a row from edwExperiment table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwExperiment *edwExperimentLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwExperiment from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwExperimentFreeList(). */ void edwExperimentSaveToDb(struct sqlConnection *conn, struct edwExperiment *el, char *tableName, int updateSize); /* Save edwExperiment as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwExperiment *edwExperimentLoad(char **row); /* Load a edwExperiment from row fetched with select * from edwExperiment * from database. Dispose of this with edwExperimentFree(). */ struct edwExperiment *edwExperimentLoadAll(char *fileName); /* Load all edwExperiment from whitespace-separated file. * Dispose of this with edwExperimentFreeList(). */ struct edwExperiment *edwExperimentLoadAllByChar(char *fileName, char chopper); /* Load all edwExperiment from chopper separated file. * Dispose of this with edwExperimentFreeList(). */ #define edwExperimentLoadAllByTab(a) edwExperimentLoadAllByChar(a, '\t'); /* Load all edwExperiment from tab separated file. * Dispose of this with edwExperimentFreeList(). */ struct edwExperiment *edwExperimentCommaIn(char **pS, struct edwExperiment *ret); /* Create a edwExperiment out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwExperiment */ void edwExperimentFree(struct edwExperiment **pEl); /* Free a single dynamically allocated edwExperiment such as created * with edwExperimentLoad(). */ void edwExperimentFreeList(struct edwExperiment **pList); /* Free a list of dynamically allocated edwExperiment's */ void edwExperimentOutput(struct edwExperiment *el, FILE *f, char sep, char lastSep); /* Print out edwExperiment. Separate fields with sep. Follow last field with lastSep. */ #define edwExperimentTabOut(el,f) edwExperimentOutput(el,f,'\t','\n'); /* Print out edwExperiment as a line in a tab-separated file. */ #define edwExperimentCommaOut(el,f) edwExperimentOutput(el,f,',',','); /* Print out edwExperiment as a comma separated list including final comma. */ #define EDWVALIDFILE_NUM_COLS 24 extern char *edwValidFileCommaSepFieldNames; struct edwValidFile /* A file that has been uploaded, the format checked, and for which at least minimal metadata exists */ { struct edwValidFile *next; /* Next in singly linked list. */ unsigned id; /* ID of validated file */ char licensePlate[17]; /* A abc123 looking license-platish thing. */ unsigned fileId; /* Pointer to file in main file table */ char *format; /* What format it's in from manifest */ char *outputType; /* What output_type it is from manifest */ char *experiment; /* What experiment it's in from manifest */ char *replicate; /* What replicate it is from manifest. Values 1,2,3... pooled, or '' */ char *validKey; /* The valid_key tag from manifest */ char *enrichedIn; /* The enriched_in tag from manifest */ char *ucscDb; /* Something like hg19 or mm9 */ long long itemCount; /* # of items in file: reads for fastqs, lines for beds, bases w/data for wig. */ long long basesInItems; /* # of bases in items */ long long sampleCount; /* # of items in sample if we are just subsampling as we do for reads. */ long long basesInSample; /* # of bases in our sample */ char *sampleBed; /* Path to a temporary bed file holding sample items */ double mapRatio; /* Proportion of items that map to genome */ double sampleCoverage; /* Proportion of assembly covered by at least one item in sample */ double depth; /* Estimated genome-equivalents covered by possibly overlapping data */ signed char singleQaStatus; /* 0 = untested, 1 = pass, -1 = fail, 2 = forced pass, -2 = forced fail */ signed char replicateQaStatus; /* 0 = untested, 1 = pass, -1 = fail, 2 = forced pass, -2 = forced fail */ char *technicalReplicate; /* Manifest's technical_replicate tag. Values 1,2,3... pooled or '' */ char *pairedEnd; /* The paired_end tag from the manifest. Values 1,2 or '' */ signed char qaVersion; /* Version of QA pipeline making status decisions */ double uniqueMapRatio; /* Fraction of reads that map uniquely to genome for bams and fastqs */ }; void edwValidFileStaticLoad(char **row, struct edwValidFile *ret); /* Load a row from edwValidFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwValidFile *edwValidFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwValidFile from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwValidFileFreeList(). */ void edwValidFileSaveToDb(struct sqlConnection *conn, struct edwValidFile *el, char *tableName, int updateSize); /* Save edwValidFile as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwValidFile *edwValidFileLoad(char **row); /* Load a edwValidFile from row fetched with select * from edwValidFile * from database. Dispose of this with edwValidFileFree(). */ struct edwValidFile *edwValidFileLoadAll(char *fileName); /* Load all edwValidFile from whitespace-separated file. * Dispose of this with edwValidFileFreeList(). */ struct edwValidFile *edwValidFileLoadAllByChar(char *fileName, char chopper); /* Load all edwValidFile from chopper separated file. * Dispose of this with edwValidFileFreeList(). */ #define edwValidFileLoadAllByTab(a) edwValidFileLoadAllByChar(a, '\t'); /* Load all edwValidFile from tab separated file. * Dispose of this with edwValidFileFreeList(). */ struct edwValidFile *edwValidFileCommaIn(char **pS, struct edwValidFile *ret); /* Create a edwValidFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwValidFile */ void edwValidFileFree(struct edwValidFile **pEl); /* Free a single dynamically allocated edwValidFile such as created * with edwValidFileLoad(). */ void edwValidFileFreeList(struct edwValidFile **pList); /* Free a list of dynamically allocated edwValidFile's */ void edwValidFileOutput(struct edwValidFile *el, FILE *f, char sep, char lastSep); /* Print out edwValidFile. Separate fields with sep. Follow last field with lastSep. */ #define edwValidFileTabOut(el,f) edwValidFileOutput(el,f,'\t','\n'); /* Print out edwValidFile as a line in a tab-separated file. */ #define edwValidFileCommaOut(el,f) edwValidFileOutput(el,f,',',','); /* Print out edwValidFile as a comma separated list including final comma. */ #define EDWFASTQFILE_NUM_COLS 29 extern char *edwFastqFileCommaSepFieldNames; struct edwFastqFile /* info on a file in fastq short read format beyond what's in edwValidFile */ { struct edwFastqFile *next; /* Next in singly linked list. */ unsigned id; /* ID in this table */ unsigned fileId; /* ID in edwFile table */ long long sampleCount; /* # of reads in sample. */ long long basesInSample; /* # of bases in sample. */ char *sampleFileName; /* Name of file containing sampleCount randomly selected items from file. */ long long readCount; /* # of reads in file */ long long baseCount; /* # of bases in all reads added up */ double readSizeMean; /* Average read size */ double readSizeStd; /* Standard deviation of read size */ int readSizeMin; /* Minimum read size */ int readSizeMax; /* Maximum read size */ double qualMean; /* Mean quality scored as 10*-log10(errorProbability) or close to it. >25 is good */ double qualStd; /* Standard deviation of quality */ double qualMin; /* Minimum observed quality */ double qualMax; /* Maximum observed quality */ char *qualType; /* For fastq files either 'sanger' or 'illumina' */ int qualZero; /* For fastq files offset to get to zero value in ascii encoding */ double atRatio; /* Ratio of A+T to total sequence (not including Ns) */ double aRatio; /* Ratio of A to total sequence (including Ns) */ double cRatio; /* Ratio of C to total sequence (including Ns) */ double gRatio; /* Ratio of G to total sequence (including Ns) */ double tRatio; /* Ratio of T to total sequence (including Ns) */ double nRatio; /* Ratio of N or . to total sequence */ double *qualPos; /* Mean value for each position in a read up to some max. */ double *aAtPos; /* % of As at each pos */ double *cAtPos; /* % of Cs at each pos */ double *gAtPos; /* % of Gs at each pos */ double *tAtPos; /* % of Ts at each pos */ double *nAtPos; /* % of '.' or 'N' at each pos */ }; struct edwFastqFile *edwFastqFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwFastqFile from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwFastqFileFreeList(). */ void edwFastqFileSaveToDb(struct sqlConnection *conn, struct edwFastqFile *el, char *tableName, int updateSize); /* Save edwFastqFile as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwFastqFile *edwFastqFileLoad(char **row); /* Load a edwFastqFile from row fetched with select * from edwFastqFile * from database. Dispose of this with edwFastqFileFree(). */ struct edwFastqFile *edwFastqFileLoadAll(char *fileName); /* Load all edwFastqFile from whitespace-separated file. * Dispose of this with edwFastqFileFreeList(). */ struct edwFastqFile *edwFastqFileLoadAllByChar(char *fileName, char chopper); /* Load all edwFastqFile from chopper separated file. * Dispose of this with edwFastqFileFreeList(). */ #define edwFastqFileLoadAllByTab(a) edwFastqFileLoadAllByChar(a, '\t'); /* Load all edwFastqFile from tab separated file. * Dispose of this with edwFastqFileFreeList(). */ struct edwFastqFile *edwFastqFileCommaIn(char **pS, struct edwFastqFile *ret); /* Create a edwFastqFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwFastqFile */ void edwFastqFileFree(struct edwFastqFile **pEl); /* Free a single dynamically allocated edwFastqFile such as created * with edwFastqFileLoad(). */ void edwFastqFileFreeList(struct edwFastqFile **pList); /* Free a list of dynamically allocated edwFastqFile's */ void edwFastqFileOutput(struct edwFastqFile *el, FILE *f, char sep, char lastSep); /* Print out edwFastqFile. Separate fields with sep. Follow last field with lastSep. */ #define edwFastqFileTabOut(el,f) edwFastqFileOutput(el,f,'\t','\n'); /* Print out edwFastqFile as a line in a tab-separated file. */ #define edwFastqFileCommaOut(el,f) edwFastqFileOutput(el,f,',',','); /* Print out edwFastqFile as a comma separated list including final comma. */ #define EDWBAMFILE_NUM_COLS 17 extern char *edwBamFileCommaSepFieldNames; struct edwBamFile /* Info on what is in a bam file beyond whet's in edwValidFile */ { struct edwBamFile *next; /* Next in singly linked list. */ unsigned id; /* ID in this table */ unsigned fileId; /* ID in edwFile table. */ signed char isPaired; /* Set to 1 if paired reads, 0 if single */ signed char isSortedByTarget; /* Set to 1 if sorted by target,pos */ long long readCount; /* # of reads in file */ long long readBaseCount; /* # of bases in all reads added up */ long long mappedCount; /* # of reads that map */ long long uniqueMappedCount; /* # of reads that map to a unique position */ double readSizeMean; /* Average read size */ double readSizeStd; /* Standard deviation of read size */ int readSizeMin; /* Minimum read size */ int readSizeMax; /* Maximum read size */ int u4mReadCount; /* Uniquely-mapped 4 million read actual read # (usually 4M) */ int u4mUniquePos; /* Unique positions in target of the 4M reads that map to single pos */ double u4mUniqueRatio; /* u4mUniqPos/u4mReadCount - measures library diversity */ long long targetBaseCount; /* Count of bases in mapping target */ unsigned targetSeqCount; /* Number of chromosomes or other distinct sequences in mapping target */ }; void edwBamFileStaticLoad(char **row, struct edwBamFile *ret); /* Load a row from edwBamFile table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwBamFile *edwBamFileLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwBamFile from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwBamFileFreeList(). */ void edwBamFileSaveToDb(struct sqlConnection *conn, struct edwBamFile *el, char *tableName, int updateSize); /* Save edwBamFile as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwBamFile *edwBamFileLoad(char **row); /* Load a edwBamFile from row fetched with select * from edwBamFile * from database. Dispose of this with edwBamFileFree(). */ struct edwBamFile *edwBamFileLoadAll(char *fileName); /* Load all edwBamFile from whitespace-separated file. * Dispose of this with edwBamFileFreeList(). */ struct edwBamFile *edwBamFileLoadAllByChar(char *fileName, char chopper); /* Load all edwBamFile from chopper separated file. * Dispose of this with edwBamFileFreeList(). */ #define edwBamFileLoadAllByTab(a) edwBamFileLoadAllByChar(a, '\t'); /* Load all edwBamFile from tab separated file. * Dispose of this with edwBamFileFreeList(). */ struct edwBamFile *edwBamFileCommaIn(char **pS, struct edwBamFile *ret); /* Create a edwBamFile out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwBamFile */ void edwBamFileFree(struct edwBamFile **pEl); /* Free a single dynamically allocated edwBamFile such as created * with edwBamFileLoad(). */ void edwBamFileFreeList(struct edwBamFile **pList); /* Free a list of dynamically allocated edwBamFile's */ void edwBamFileOutput(struct edwBamFile *el, FILE *f, char sep, char lastSep); /* Print out edwBamFile. Separate fields with sep. Follow last field with lastSep. */ #define edwBamFileTabOut(el,f) edwBamFileOutput(el,f,'\t','\n'); /* Print out edwBamFile as a line in a tab-separated file. */ #define edwBamFileCommaOut(el,f) edwBamFileOutput(el,f,',',','); /* Print out edwBamFile as a comma separated list including final comma. */ #define EDWQAFAIL_NUM_COLS 4 extern char *edwQaFailCommaSepFieldNames; struct edwQaFail /* Record of a QA failure. */ { struct edwQaFail *next; /* Next in singly linked list. */ unsigned id; /* ID of failure */ unsigned fileId; /* File that failed */ unsigned qaVersion; /* QA pipeline version */ char *reason; /* reason for failure */ }; void edwQaFailStaticLoad(char **row, struct edwQaFail *ret); /* Load a row from edwQaFail table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaFail *edwQaFailLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaFail from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaFailFreeList(). */ void edwQaFailSaveToDb(struct sqlConnection *conn, struct edwQaFail *el, char *tableName, int updateSize); /* Save edwQaFail as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaFail *edwQaFailLoad(char **row); /* Load a edwQaFail from row fetched with select * from edwQaFail * from database. Dispose of this with edwQaFailFree(). */ struct edwQaFail *edwQaFailLoadAll(char *fileName); /* Load all edwQaFail from whitespace-separated file. * Dispose of this with edwQaFailFreeList(). */ struct edwQaFail *edwQaFailLoadAllByChar(char *fileName, char chopper); /* Load all edwQaFail from chopper separated file. * Dispose of this with edwQaFailFreeList(). */ #define edwQaFailLoadAllByTab(a) edwQaFailLoadAllByChar(a, '\t'); /* Load all edwQaFail from tab separated file. * Dispose of this with edwQaFailFreeList(). */ struct edwQaFail *edwQaFailCommaIn(char **pS, struct edwQaFail *ret); /* Create a edwQaFail out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaFail */ void edwQaFailFree(struct edwQaFail **pEl); /* Free a single dynamically allocated edwQaFail such as created * with edwQaFailLoad(). */ void edwQaFailFreeList(struct edwQaFail **pList); /* Free a list of dynamically allocated edwQaFail's */ void edwQaFailOutput(struct edwQaFail *el, FILE *f, char sep, char lastSep); /* Print out edwQaFail. Separate fields with sep. Follow last field with lastSep. */ #define edwQaFailTabOut(el,f) edwQaFailOutput(el,f,'\t','\n'); /* Print out edwQaFail as a line in a tab-separated file. */ #define edwQaFailCommaOut(el,f) edwQaFailOutput(el,f,',',','); /* Print out edwQaFail as a comma separated list including final comma. */ #define EDWQAENRICHTARGET_NUM_COLS 5 extern char *edwQaEnrichTargetCommaSepFieldNames; struct edwQaEnrichTarget /* A target for our enrichment analysis. */ { struct edwQaEnrichTarget *next; /* Next in singly linked list. */ unsigned id; /* ID of this enrichment target */ unsigned assemblyId; /* Which assembly this goes to */ char *name; /* Something like 'exon' or 'promoter' */ unsigned fileId; /* A simple BED 3 format file that defines target. Bases covered are unique */ long long targetSize; /* Total number of bases covered by target */ }; void edwQaEnrichTargetStaticLoad(char **row, struct edwQaEnrichTarget *ret); /* Load a row from edwQaEnrichTarget table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaEnrichTarget *edwQaEnrichTargetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaEnrichTarget from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaEnrichTargetFreeList(). */ void edwQaEnrichTargetSaveToDb(struct sqlConnection *conn, struct edwQaEnrichTarget *el, char *tableName, int updateSize); /* Save edwQaEnrichTarget as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaEnrichTarget *edwQaEnrichTargetLoad(char **row); /* Load a edwQaEnrichTarget from row fetched with select * from edwQaEnrichTarget * from database. Dispose of this with edwQaEnrichTargetFree(). */ struct edwQaEnrichTarget *edwQaEnrichTargetLoadAll(char *fileName); /* Load all edwQaEnrichTarget from whitespace-separated file. * Dispose of this with edwQaEnrichTargetFreeList(). */ struct edwQaEnrichTarget *edwQaEnrichTargetLoadAllByChar(char *fileName, char chopper); /* Load all edwQaEnrichTarget from chopper separated file. * Dispose of this with edwQaEnrichTargetFreeList(). */ #define edwQaEnrichTargetLoadAllByTab(a) edwQaEnrichTargetLoadAllByChar(a, '\t'); /* Load all edwQaEnrichTarget from tab separated file. * Dispose of this with edwQaEnrichTargetFreeList(). */ struct edwQaEnrichTarget *edwQaEnrichTargetCommaIn(char **pS, struct edwQaEnrichTarget *ret); /* Create a edwQaEnrichTarget out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaEnrichTarget */ void edwQaEnrichTargetFree(struct edwQaEnrichTarget **pEl); /* Free a single dynamically allocated edwQaEnrichTarget such as created * with edwQaEnrichTargetLoad(). */ void edwQaEnrichTargetFreeList(struct edwQaEnrichTarget **pList); /* Free a list of dynamically allocated edwQaEnrichTarget's */ void edwQaEnrichTargetOutput(struct edwQaEnrichTarget *el, FILE *f, char sep, char lastSep); /* Print out edwQaEnrichTarget. Separate fields with sep. Follow last field with lastSep. */ #define edwQaEnrichTargetTabOut(el,f) edwQaEnrichTargetOutput(el,f,'\t','\n'); /* Print out edwQaEnrichTarget as a line in a tab-separated file. */ #define edwQaEnrichTargetCommaOut(el,f) edwQaEnrichTargetOutput(el,f,',',','); /* Print out edwQaEnrichTarget as a comma separated list including final comma. */ #define EDWQAENRICH_NUM_COLS 8 extern char *edwQaEnrichCommaSepFieldNames; struct edwQaEnrich /* An enrichment analysis applied to file. */ { struct edwQaEnrich *next; /* Next in singly linked list. */ unsigned id; /* ID of this enrichment analysis */ unsigned fileId; /* File we are looking at skeptically */ unsigned qaEnrichTargetId; /* Information about a target for this analysis */ long long targetBaseHits; /* Number of hits to bases in target */ long long targetUniqHits; /* Number of unique bases hit in target */ double coverage; /* Coverage of target - just targetUniqHits/targetSize */ double enrichment; /* Amount we hit target/amount we hit genome */ double uniqEnrich; /* coverage/sampleCoverage */ }; void edwQaEnrichStaticLoad(char **row, struct edwQaEnrich *ret); /* Load a row from edwQaEnrich table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaEnrich *edwQaEnrichLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaEnrich from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaEnrichFreeList(). */ void edwQaEnrichSaveToDb(struct sqlConnection *conn, struct edwQaEnrich *el, char *tableName, int updateSize); /* Save edwQaEnrich as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaEnrich *edwQaEnrichLoad(char **row); /* Load a edwQaEnrich from row fetched with select * from edwQaEnrich * from database. Dispose of this with edwQaEnrichFree(). */ struct edwQaEnrich *edwQaEnrichLoadAll(char *fileName); /* Load all edwQaEnrich from whitespace-separated file. * Dispose of this with edwQaEnrichFreeList(). */ struct edwQaEnrich *edwQaEnrichLoadAllByChar(char *fileName, char chopper); /* Load all edwQaEnrich from chopper separated file. * Dispose of this with edwQaEnrichFreeList(). */ #define edwQaEnrichLoadAllByTab(a) edwQaEnrichLoadAllByChar(a, '\t'); /* Load all edwQaEnrich from tab separated file. * Dispose of this with edwQaEnrichFreeList(). */ struct edwQaEnrich *edwQaEnrichCommaIn(char **pS, struct edwQaEnrich *ret); /* Create a edwQaEnrich out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaEnrich */ void edwQaEnrichFree(struct edwQaEnrich **pEl); /* Free a single dynamically allocated edwQaEnrich such as created * with edwQaEnrichLoad(). */ void edwQaEnrichFreeList(struct edwQaEnrich **pList); /* Free a list of dynamically allocated edwQaEnrich's */ void edwQaEnrichOutput(struct edwQaEnrich *el, FILE *f, char sep, char lastSep); /* Print out edwQaEnrich. Separate fields with sep. Follow last field with lastSep. */ #define edwQaEnrichTabOut(el,f) edwQaEnrichOutput(el,f,'\t','\n'); /* Print out edwQaEnrich as a line in a tab-separated file. */ #define edwQaEnrichCommaOut(el,f) edwQaEnrichOutput(el,f,',',','); /* Print out edwQaEnrich as a comma separated list including final comma. */ #define EDWQACONTAMTARGET_NUM_COLS 2 extern char *edwQaContamTargetCommaSepFieldNames; struct edwQaContamTarget /* A target for our contamination analysis. */ { struct edwQaContamTarget *next; /* Next in singly linked list. */ unsigned id; /* ID of this contamination target */ unsigned assemblyId; /* Assembly we're aligning against to check for contamination. */ }; void edwQaContamTargetStaticLoad(char **row, struct edwQaContamTarget *ret); /* Load a row from edwQaContamTarget table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaContamTarget *edwQaContamTargetLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaContamTarget from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaContamTargetFreeList(). */ void edwQaContamTargetSaveToDb(struct sqlConnection *conn, struct edwQaContamTarget *el, char *tableName, int updateSize); /* Save edwQaContamTarget as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaContamTarget *edwQaContamTargetLoad(char **row); /* Load a edwQaContamTarget from row fetched with select * from edwQaContamTarget * from database. Dispose of this with edwQaContamTargetFree(). */ struct edwQaContamTarget *edwQaContamTargetLoadAll(char *fileName); /* Load all edwQaContamTarget from whitespace-separated file. * Dispose of this with edwQaContamTargetFreeList(). */ struct edwQaContamTarget *edwQaContamTargetLoadAllByChar(char *fileName, char chopper); /* Load all edwQaContamTarget from chopper separated file. * Dispose of this with edwQaContamTargetFreeList(). */ #define edwQaContamTargetLoadAllByTab(a) edwQaContamTargetLoadAllByChar(a, '\t'); /* Load all edwQaContamTarget from tab separated file. * Dispose of this with edwQaContamTargetFreeList(). */ struct edwQaContamTarget *edwQaContamTargetCommaIn(char **pS, struct edwQaContamTarget *ret); /* Create a edwQaContamTarget out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaContamTarget */ void edwQaContamTargetFree(struct edwQaContamTarget **pEl); /* Free a single dynamically allocated edwQaContamTarget such as created * with edwQaContamTargetLoad(). */ void edwQaContamTargetFreeList(struct edwQaContamTarget **pList); /* Free a list of dynamically allocated edwQaContamTarget's */ void edwQaContamTargetOutput(struct edwQaContamTarget *el, FILE *f, char sep, char lastSep); /* Print out edwQaContamTarget. Separate fields with sep. Follow last field with lastSep. */ #define edwQaContamTargetTabOut(el,f) edwQaContamTargetOutput(el,f,'\t','\n'); /* Print out edwQaContamTarget as a line in a tab-separated file. */ #define edwQaContamTargetCommaOut(el,f) edwQaContamTargetOutput(el,f,',',','); /* Print out edwQaContamTarget as a comma separated list including final comma. */ #define EDWQACONTAM_NUM_COLS 4 extern char *edwQaContamCommaSepFieldNames; struct edwQaContam /* Results of contamination analysis of one file against one target */ { struct edwQaContam *next; /* Next in singly linked list. */ unsigned id; /* ID of this contamination analysis */ unsigned fileId; /* File we are looking at skeptically */ unsigned qaContamTargetId; /* Information about a target for this analysis */ double mapRatio; /* Proportion of items that map to target */ }; void edwQaContamStaticLoad(char **row, struct edwQaContam *ret); /* Load a row from edwQaContam table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaContam *edwQaContamLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaContam from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaContamFreeList(). */ void edwQaContamSaveToDb(struct sqlConnection *conn, struct edwQaContam *el, char *tableName, int updateSize); /* Save edwQaContam as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaContam *edwQaContamLoad(char **row); /* Load a edwQaContam from row fetched with select * from edwQaContam * from database. Dispose of this with edwQaContamFree(). */ struct edwQaContam *edwQaContamLoadAll(char *fileName); /* Load all edwQaContam from whitespace-separated file. * Dispose of this with edwQaContamFreeList(). */ struct edwQaContam *edwQaContamLoadAllByChar(char *fileName, char chopper); /* Load all edwQaContam from chopper separated file. * Dispose of this with edwQaContamFreeList(). */ #define edwQaContamLoadAllByTab(a) edwQaContamLoadAllByChar(a, '\t'); /* Load all edwQaContam from tab separated file. * Dispose of this with edwQaContamFreeList(). */ struct edwQaContam *edwQaContamCommaIn(char **pS, struct edwQaContam *ret); /* Create a edwQaContam out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaContam */ void edwQaContamFree(struct edwQaContam **pEl); /* Free a single dynamically allocated edwQaContam such as created * with edwQaContamLoad(). */ void edwQaContamFreeList(struct edwQaContam **pList); /* Free a list of dynamically allocated edwQaContam's */ void edwQaContamOutput(struct edwQaContam *el, FILE *f, char sep, char lastSep); /* Print out edwQaContam. Separate fields with sep. Follow last field with lastSep. */ #define edwQaContamTabOut(el,f) edwQaContamOutput(el,f,'\t','\n'); /* Print out edwQaContam as a line in a tab-separated file. */ #define edwQaContamCommaOut(el,f) edwQaContamOutput(el,f,',',','); /* Print out edwQaContam as a comma separated list including final comma. */ #define EDWQAREPEAT_NUM_COLS 4 extern char *edwQaRepeatCommaSepFieldNames; struct edwQaRepeat /* What percentage of data set aligns to various repeat classes. */ { struct edwQaRepeat *next; /* Next in singly linked list. */ unsigned id; /* ID of this repeat analysis. */ unsigned fileId; /* File we are analysing. */ char *repeatClass; /* RepeatMasker high end classification, or 'total' for all repeats. */ double mapRatio; /* Proportion that map to this repeat. */ }; void edwQaRepeatStaticLoad(char **row, struct edwQaRepeat *ret); /* Load a row from edwQaRepeat table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaRepeat *edwQaRepeatLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaRepeat from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaRepeatFreeList(). */ void edwQaRepeatSaveToDb(struct sqlConnection *conn, struct edwQaRepeat *el, char *tableName, int updateSize); /* Save edwQaRepeat as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaRepeat *edwQaRepeatLoad(char **row); /* Load a edwQaRepeat from row fetched with select * from edwQaRepeat * from database. Dispose of this with edwQaRepeatFree(). */ struct edwQaRepeat *edwQaRepeatLoadAll(char *fileName); /* Load all edwQaRepeat from whitespace-separated file. * Dispose of this with edwQaRepeatFreeList(). */ struct edwQaRepeat *edwQaRepeatLoadAllByChar(char *fileName, char chopper); /* Load all edwQaRepeat from chopper separated file. * Dispose of this with edwQaRepeatFreeList(). */ #define edwQaRepeatLoadAllByTab(a) edwQaRepeatLoadAllByChar(a, '\t'); /* Load all edwQaRepeat from tab separated file. * Dispose of this with edwQaRepeatFreeList(). */ struct edwQaRepeat *edwQaRepeatCommaIn(char **pS, struct edwQaRepeat *ret); /* Create a edwQaRepeat out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaRepeat */ void edwQaRepeatFree(struct edwQaRepeat **pEl); /* Free a single dynamically allocated edwQaRepeat such as created * with edwQaRepeatLoad(). */ void edwQaRepeatFreeList(struct edwQaRepeat **pList); /* Free a list of dynamically allocated edwQaRepeat's */ void edwQaRepeatOutput(struct edwQaRepeat *el, FILE *f, char sep, char lastSep); /* Print out edwQaRepeat. Separate fields with sep. Follow last field with lastSep. */ #define edwQaRepeatTabOut(el,f) edwQaRepeatOutput(el,f,'\t','\n'); /* Print out edwQaRepeat as a line in a tab-separated file. */ #define edwQaRepeatCommaOut(el,f) edwQaRepeatOutput(el,f,',',','); /* Print out edwQaRepeat as a comma separated list including final comma. */ #define EDWQAPAIRSAMPLEOVERLAP_NUM_COLS 7 extern char *edwQaPairSampleOverlapCommaSepFieldNames; struct edwQaPairSampleOverlap /* A comparison of the amount of overlap between two samples that cover ~0.1% to 10% of target. */ { struct edwQaPairSampleOverlap *next; /* Next in singly linked list. */ unsigned id; /* Id of this qa pair */ unsigned elderFileId; /* Id of elder (smaller fileId) in correlated pair */ unsigned youngerFileId; /* Id of younger (larger fileId) in correlated pair */ long long elderSampleBases; /* Number of bases in elder sample */ long long youngerSampleBases; /* Number of bases in younger sample */ long long sampleOverlapBases; /* Number of bases that overlap between younger and elder sample */ double sampleSampleEnrichment; /* Amount samples overlap more than expected. */ }; void edwQaPairSampleOverlapStaticLoad(char **row, struct edwQaPairSampleOverlap *ret); /* Load a row from edwQaPairSampleOverlap table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaPairSampleOverlap *edwQaPairSampleOverlapLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaPairSampleOverlap from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaPairSampleOverlapFreeList(). */ void edwQaPairSampleOverlapSaveToDb(struct sqlConnection *conn, struct edwQaPairSampleOverlap *el, char *tableName, int updateSize); /* Save edwQaPairSampleOverlap as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaPairSampleOverlap *edwQaPairSampleOverlapLoad(char **row); /* Load a edwQaPairSampleOverlap from row fetched with select * from edwQaPairSampleOverlap * from database. Dispose of this with edwQaPairSampleOverlapFree(). */ struct edwQaPairSampleOverlap *edwQaPairSampleOverlapLoadAll(char *fileName); /* Load all edwQaPairSampleOverlap from whitespace-separated file. * Dispose of this with edwQaPairSampleOverlapFreeList(). */ struct edwQaPairSampleOverlap *edwQaPairSampleOverlapLoadAllByChar(char *fileName, char chopper); /* Load all edwQaPairSampleOverlap from chopper separated file. * Dispose of this with edwQaPairSampleOverlapFreeList(). */ #define edwQaPairSampleOverlapLoadAllByTab(a) edwQaPairSampleOverlapLoadAllByChar(a, '\t'); /* Load all edwQaPairSampleOverlap from tab separated file. * Dispose of this with edwQaPairSampleOverlapFreeList(). */ struct edwQaPairSampleOverlap *edwQaPairSampleOverlapCommaIn(char **pS, struct edwQaPairSampleOverlap *ret); /* Create a edwQaPairSampleOverlap out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaPairSampleOverlap */ void edwQaPairSampleOverlapFree(struct edwQaPairSampleOverlap **pEl); /* Free a single dynamically allocated edwQaPairSampleOverlap such as created * with edwQaPairSampleOverlapLoad(). */ void edwQaPairSampleOverlapFreeList(struct edwQaPairSampleOverlap **pList); /* Free a list of dynamically allocated edwQaPairSampleOverlap's */ void edwQaPairSampleOverlapOutput(struct edwQaPairSampleOverlap *el, FILE *f, char sep, char lastSep); /* Print out edwQaPairSampleOverlap. Separate fields with sep. Follow last field with lastSep. */ #define edwQaPairSampleOverlapTabOut(el,f) edwQaPairSampleOverlapOutput(el,f,'\t','\n'); /* Print out edwQaPairSampleOverlap as a line in a tab-separated file. */ #define edwQaPairSampleOverlapCommaOut(el,f) edwQaPairSampleOverlapOutput(el,f,',',','); /* Print out edwQaPairSampleOverlap as a comma separated list including final comma. */ #define EDWQAPAIRCORRELATION_NUM_COLS 6 extern char *edwQaPairCorrelationCommaSepFieldNames; struct edwQaPairCorrelation /* A correlation between two files of the same type. */ { struct edwQaPairCorrelation *next; /* Next in singly linked list. */ unsigned id; /* Id of this correlation pair */ unsigned elderFileId; /* Id of elder (smaller fileId) in correlated pair */ unsigned youngerFileId; /* Id of younger (larger fileId) in correlated pair */ double pearsonInEnriched; /* Pearson's R inside enriched areas where there is overlap */ double pearsonOverall; /* Pearson's R over all places where both have data */ double pearsonClipped; /* Pearson's R clipped at two standard deviations up from the mean */ }; void edwQaPairCorrelationStaticLoad(char **row, struct edwQaPairCorrelation *ret); /* Load a row from edwQaPairCorrelation table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaPairCorrelation *edwQaPairCorrelationLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaPairCorrelation from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaPairCorrelationFreeList(). */ void edwQaPairCorrelationSaveToDb(struct sqlConnection *conn, struct edwQaPairCorrelation *el, char *tableName, int updateSize); /* Save edwQaPairCorrelation as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaPairCorrelation *edwQaPairCorrelationLoad(char **row); /* Load a edwQaPairCorrelation from row fetched with select * from edwQaPairCorrelation * from database. Dispose of this with edwQaPairCorrelationFree(). */ struct edwQaPairCorrelation *edwQaPairCorrelationLoadAll(char *fileName); /* Load all edwQaPairCorrelation from whitespace-separated file. * Dispose of this with edwQaPairCorrelationFreeList(). */ struct edwQaPairCorrelation *edwQaPairCorrelationLoadAllByChar(char *fileName, char chopper); /* Load all edwQaPairCorrelation from chopper separated file. * Dispose of this with edwQaPairCorrelationFreeList(). */ #define edwQaPairCorrelationLoadAllByTab(a) edwQaPairCorrelationLoadAllByChar(a, '\t'); /* Load all edwQaPairCorrelation from tab separated file. * Dispose of this with edwQaPairCorrelationFreeList(). */ struct edwQaPairCorrelation *edwQaPairCorrelationCommaIn(char **pS, struct edwQaPairCorrelation *ret); /* Create a edwQaPairCorrelation out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaPairCorrelation */ void edwQaPairCorrelationFree(struct edwQaPairCorrelation **pEl); /* Free a single dynamically allocated edwQaPairCorrelation such as created * with edwQaPairCorrelationLoad(). */ void edwQaPairCorrelationFreeList(struct edwQaPairCorrelation **pList); /* Free a list of dynamically allocated edwQaPairCorrelation's */ void edwQaPairCorrelationOutput(struct edwQaPairCorrelation *el, FILE *f, char sep, char lastSep); /* Print out edwQaPairCorrelation. Separate fields with sep. Follow last field with lastSep. */ #define edwQaPairCorrelationTabOut(el,f) edwQaPairCorrelationOutput(el,f,'\t','\n'); /* Print out edwQaPairCorrelation as a line in a tab-separated file. */ #define edwQaPairCorrelationCommaOut(el,f) edwQaPairCorrelationOutput(el,f,',',','); /* Print out edwQaPairCorrelation as a comma separated list including final comma. */ #define EDWQAPAIREDENDFASTQ_NUM_COLS 9 extern char *edwQaPairedEndFastqCommaSepFieldNames; struct edwQaPairedEndFastq /* Information about two paired-end fastqs */ { struct edwQaPairedEndFastq *next; /* Next in singly linked list. */ unsigned id; /* Id of this set of paired end files */ unsigned fileId1; /* Id of first in pair */ unsigned fileId2; /* Id of second in pair */ double concordance; /* % of uniquely aligning reads where pairs nearby and point right way */ double distanceMean; /* Average distance between reads */ double distanceStd; /* Standard deviation of distance */ double distanceMin; /* Minimum distance */ double distanceMax; /* Maximum distatnce */ signed char recordComplete; /* Flag to avoid a race condition. Ignore record if this is 0 */ }; void edwQaPairedEndFastqStaticLoad(char **row, struct edwQaPairedEndFastq *ret); /* Load a row from edwQaPairedEndFastq table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaPairedEndFastq *edwQaPairedEndFastqLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaPairedEndFastq from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaPairedEndFastqFreeList(). */ void edwQaPairedEndFastqSaveToDb(struct sqlConnection *conn, struct edwQaPairedEndFastq *el, char *tableName, int updateSize); /* Save edwQaPairedEndFastq as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaPairedEndFastq *edwQaPairedEndFastqLoad(char **row); /* Load a edwQaPairedEndFastq from row fetched with select * from edwQaPairedEndFastq * from database. Dispose of this with edwQaPairedEndFastqFree(). */ struct edwQaPairedEndFastq *edwQaPairedEndFastqLoadAll(char *fileName); /* Load all edwQaPairedEndFastq from whitespace-separated file. * Dispose of this with edwQaPairedEndFastqFreeList(). */ struct edwQaPairedEndFastq *edwQaPairedEndFastqLoadAllByChar(char *fileName, char chopper); /* Load all edwQaPairedEndFastq from chopper separated file. * Dispose of this with edwQaPairedEndFastqFreeList(). */ #define edwQaPairedEndFastqLoadAllByTab(a) edwQaPairedEndFastqLoadAllByChar(a, '\t'); /* Load all edwQaPairedEndFastq from tab separated file. * Dispose of this with edwQaPairedEndFastqFreeList(). */ struct edwQaPairedEndFastq *edwQaPairedEndFastqCommaIn(char **pS, struct edwQaPairedEndFastq *ret); /* Create a edwQaPairedEndFastq out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaPairedEndFastq */ void edwQaPairedEndFastqFree(struct edwQaPairedEndFastq **pEl); /* Free a single dynamically allocated edwQaPairedEndFastq such as created * with edwQaPairedEndFastqLoad(). */ void edwQaPairedEndFastqFreeList(struct edwQaPairedEndFastq **pList); /* Free a list of dynamically allocated edwQaPairedEndFastq's */ void edwQaPairedEndFastqOutput(struct edwQaPairedEndFastq *el, FILE *f, char sep, char lastSep); /* Print out edwQaPairedEndFastq. Separate fields with sep. Follow last field with lastSep. */ #define edwQaPairedEndFastqTabOut(el,f) edwQaPairedEndFastqOutput(el,f,'\t','\n'); /* Print out edwQaPairedEndFastq as a line in a tab-separated file. */ #define edwQaPairedEndFastqCommaOut(el,f) edwQaPairedEndFastqOutput(el,f,',',','); /* Print out edwQaPairedEndFastq as a comma separated list including final comma. */ #define EDWQAWIGSPOT_NUM_COLS 9 extern char *edwQaWigSpotCommaSepFieldNames; struct edwQaWigSpot /* Information about proportion of signal in a wig that lands under spots in a peak or bed file */ { struct edwQaWigSpot *next; /* Next in singly linked list. */ unsigned id; /* Id of this wig/spot intersection */ unsigned wigId; /* Id of bigWig file */ unsigned spotId; /* Id of a bigBed file probably broadPeak or narrowPeak */ double spotRatio; /* Ratio of signal in spots to total signal, between 0 and 1 */ double enrichment; /* Enrichment in spots compared to genome overall */ long long basesInGenome; /* Number of bases in genome */ long long basesInSpots; /* Number of bases in spots */ double sumSignal; /* Total signal */ double spotSumSignal; /* Total signal in spots */ }; void edwQaWigSpotStaticLoad(char **row, struct edwQaWigSpot *ret); /* Load a row from edwQaWigSpot table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaWigSpot *edwQaWigSpotLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaWigSpot from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaWigSpotFreeList(). */ void edwQaWigSpotSaveToDb(struct sqlConnection *conn, struct edwQaWigSpot *el, char *tableName, int updateSize); /* Save edwQaWigSpot as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaWigSpot *edwQaWigSpotLoad(char **row); /* Load a edwQaWigSpot from row fetched with select * from edwQaWigSpot * from database. Dispose of this with edwQaWigSpotFree(). */ struct edwQaWigSpot *edwQaWigSpotLoadAll(char *fileName); /* Load all edwQaWigSpot from whitespace-separated file. * Dispose of this with edwQaWigSpotFreeList(). */ struct edwQaWigSpot *edwQaWigSpotLoadAllByChar(char *fileName, char chopper); /* Load all edwQaWigSpot from chopper separated file. * Dispose of this with edwQaWigSpotFreeList(). */ #define edwQaWigSpotLoadAllByTab(a) edwQaWigSpotLoadAllByChar(a, '\t'); /* Load all edwQaWigSpot from tab separated file. * Dispose of this with edwQaWigSpotFreeList(). */ struct edwQaWigSpot *edwQaWigSpotCommaIn(char **pS, struct edwQaWigSpot *ret); /* Create a edwQaWigSpot out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaWigSpot */ void edwQaWigSpotFree(struct edwQaWigSpot **pEl); /* Free a single dynamically allocated edwQaWigSpot such as created * with edwQaWigSpotLoad(). */ void edwQaWigSpotFreeList(struct edwQaWigSpot **pList); /* Free a list of dynamically allocated edwQaWigSpot's */ void edwQaWigSpotOutput(struct edwQaWigSpot *el, FILE *f, char sep, char lastSep); /* Print out edwQaWigSpot. Separate fields with sep. Follow last field with lastSep. */ #define edwQaWigSpotTabOut(el,f) edwQaWigSpotOutput(el,f,'\t','\n'); /* Print out edwQaWigSpot as a line in a tab-separated file. */ #define edwQaWigSpotCommaOut(el,f) edwQaWigSpotOutput(el,f,',',','); /* Print out edwQaWigSpot as a comma separated list including final comma. */ #define EDWQADNASESINGLESTATS5M_NUM_COLS 18 extern char *edwQaDnaseSingleStats5mCommaSepFieldNames; struct edwQaDnaseSingleStats5m /* Statistics calculated based on a 5M sample of DNAse aligned reads from a bam file. */ { struct edwQaDnaseSingleStats5m *next; /* Next in singly linked list. */ unsigned id; /* Id of this row in table. */ unsigned fileId; /* Id of bam file this is calculated from */ unsigned sampleReads; /* Number of mapped reads */ double spotRatio; /* Ratio of signal in spots to total signal, between 0 and 1 */ double enrichment; /* Enrichment in spots compared to genome overall */ long long basesInGenome; /* Number of bases in genome */ long long basesInSpots; /* Number of bases in spots */ double sumSignal; /* Total signal */ double spotSumSignal; /* Total signal in spots */ char *estFragLength; /* Up to three comma separated strand cross-correlation peaks */ char *corrEstFragLen; /* Up to three cross strand correlations at the given peaks */ int phantomPeak; /* Read length/phantom peak strand shift */ double corrPhantomPeak; /* Correlation value at phantom peak */ int argMinCorr; /* strand shift at which cross-correlation is lowest */ double minCorr; /* minimum value of cross-correlation */ double nsc; /* Normalized strand cross-correlation coefficient (NSC) = corrEstFragLen/minCorr */ double rsc; /* Relative strand cross-correlation coefficient (RSC) */ int rscQualityTag; /* based on thresholded RSC (codes: -2:veryLow,-1:Low,0:Medium,1:High,2:veryHigh) */ }; void edwQaDnaseSingleStats5mStaticLoad(char **row, struct edwQaDnaseSingleStats5m *ret); /* Load a row from edwQaDnaseSingleStats5m table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwQaDnaseSingleStats5m *edwQaDnaseSingleStats5mLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwQaDnaseSingleStats5m from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwQaDnaseSingleStats5mFreeList(). */ void edwQaDnaseSingleStats5mSaveToDb(struct sqlConnection *conn, struct edwQaDnaseSingleStats5m *el, char *tableName, int updateSize); /* Save edwQaDnaseSingleStats5m as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwQaDnaseSingleStats5m *edwQaDnaseSingleStats5mLoad(char **row); /* Load a edwQaDnaseSingleStats5m from row fetched with select * from edwQaDnaseSingleStats5m * from database. Dispose of this with edwQaDnaseSingleStats5mFree(). */ struct edwQaDnaseSingleStats5m *edwQaDnaseSingleStats5mLoadAll(char *fileName); /* Load all edwQaDnaseSingleStats5m from whitespace-separated file. * Dispose of this with edwQaDnaseSingleStats5mFreeList(). */ struct edwQaDnaseSingleStats5m *edwQaDnaseSingleStats5mLoadAllByChar(char *fileName, char chopper); /* Load all edwQaDnaseSingleStats5m from chopper separated file. * Dispose of this with edwQaDnaseSingleStats5mFreeList(). */ #define edwQaDnaseSingleStats5mLoadAllByTab(a) edwQaDnaseSingleStats5mLoadAllByChar(a, '\t'); /* Load all edwQaDnaseSingleStats5m from tab separated file. * Dispose of this with edwQaDnaseSingleStats5mFreeList(). */ struct edwQaDnaseSingleStats5m *edwQaDnaseSingleStats5mCommaIn(char **pS, struct edwQaDnaseSingleStats5m *ret); /* Create a edwQaDnaseSingleStats5m out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwQaDnaseSingleStats5m */ void edwQaDnaseSingleStats5mFree(struct edwQaDnaseSingleStats5m **pEl); /* Free a single dynamically allocated edwQaDnaseSingleStats5m such as created * with edwQaDnaseSingleStats5mLoad(). */ void edwQaDnaseSingleStats5mFreeList(struct edwQaDnaseSingleStats5m **pList); /* Free a list of dynamically allocated edwQaDnaseSingleStats5m's */ void edwQaDnaseSingleStats5mOutput(struct edwQaDnaseSingleStats5m *el, FILE *f, char sep, char lastSep); /* Print out edwQaDnaseSingleStats5m. Separate fields with sep. Follow last field with lastSep. */ #define edwQaDnaseSingleStats5mTabOut(el,f) edwQaDnaseSingleStats5mOutput(el,f,'\t','\n'); /* Print out edwQaDnaseSingleStats5m as a line in a tab-separated file. */ #define edwQaDnaseSingleStats5mCommaOut(el,f) edwQaDnaseSingleStats5mOutput(el,f,',',','); /* Print out edwQaDnaseSingleStats5m as a comma separated list including final comma. */ #define EDWJOB_NUM_COLS 7 extern char *edwJobCommaSepFieldNames; struct edwJob /* A job to be run asynchronously and not too many all at once. */ { struct edwJob *next; /* Next in singly linked list. */ unsigned id; /* Job id */ char *commandLine; /* Command line of job */ long long startTime; /* Start time in seconds since 1970 */ long long endTime; /* End time in seconds since 1970 */ char *stderr; /* The output to stderr of the run - may be nonempty even with success */ int returnCode; /* The return code from system command - 0 for success */ int pid; /* Process ID for running processes */ }; void edwJobStaticLoad(char **row, struct edwJob *ret); /* Load a row from edwJob table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwJob *edwJobLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwJob from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwJobFreeList(). */ void edwJobSaveToDb(struct sqlConnection *conn, struct edwJob *el, char *tableName, int updateSize); /* Save edwJob as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwJob *edwJobLoad(char **row); /* Load a edwJob from row fetched with select * from edwJob * from database. Dispose of this with edwJobFree(). */ struct edwJob *edwJobLoadAll(char *fileName); /* Load all edwJob from whitespace-separated file. * Dispose of this with edwJobFreeList(). */ struct edwJob *edwJobLoadAllByChar(char *fileName, char chopper); /* Load all edwJob from chopper separated file. * Dispose of this with edwJobFreeList(). */ #define edwJobLoadAllByTab(a) edwJobLoadAllByChar(a, '\t'); /* Load all edwJob from tab separated file. * Dispose of this with edwJobFreeList(). */ struct edwJob *edwJobCommaIn(char **pS, struct edwJob *ret); /* Create a edwJob out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwJob */ void edwJobFree(struct edwJob **pEl); /* Free a single dynamically allocated edwJob such as created * with edwJobLoad(). */ void edwJobFreeList(struct edwJob **pList); /* Free a list of dynamically allocated edwJob's */ void edwJobOutput(struct edwJob *el, FILE *f, char sep, char lastSep); /* Print out edwJob. Separate fields with sep. Follow last field with lastSep. */ #define edwJobTabOut(el,f) edwJobOutput(el,f,'\t','\n'); /* Print out edwJob as a line in a tab-separated file. */ #define edwJobCommaOut(el,f) edwJobOutput(el,f,',',','); /* Print out edwJob as a comma separated list including final comma. */ #define EDWSUBMITJOB_NUM_COLS 7 extern char *edwSubmitJobCommaSepFieldNames; struct edwSubmitJob /* A submission job to be run asynchronously and not too many all at once. */ { struct edwSubmitJob *next; /* Next in singly linked list. */ unsigned id; /* Job id */ char *commandLine; /* Command line of job */ long long startTime; /* Start time in seconds since 1970 */ long long endTime; /* End time in seconds since 1970 */ char *stderr; /* The output to stderr of the run - may be nonempty even with success */ int returnCode; /* The return code from system command - 0 for success */ int pid; /* Process ID for running processes */ }; void edwSubmitJobStaticLoad(char **row, struct edwSubmitJob *ret); /* Load a row from edwSubmitJob table into ret. The contents of ret will * be replaced at the next call to this function. */ struct edwSubmitJob *edwSubmitJobLoadByQuery(struct sqlConnection *conn, char *query); /* Load all edwSubmitJob from table that satisfy the query given. * Where query is of the form 'select * from example where something=something' * or 'select example.* from example, anotherTable where example.something = * anotherTable.something'. * Dispose of this with edwSubmitJobFreeList(). */ void edwSubmitJobSaveToDb(struct sqlConnection *conn, struct edwSubmitJob *el, char *tableName, int updateSize); /* Save edwSubmitJob as a row to the table specified by tableName. * As blob fields may be arbitrary size updateSize specifies the approx size * of a string that would contain the entire query. Arrays of native types are * converted to comma separated strings and loaded as such, User defined types are * inserted as NULL. This function automatically escapes quoted strings for mysql. */ struct edwSubmitJob *edwSubmitJobLoad(char **row); /* Load a edwSubmitJob from row fetched with select * from edwSubmitJob * from database. Dispose of this with edwSubmitJobFree(). */ struct edwSubmitJob *edwSubmitJobLoadAll(char *fileName); /* Load all edwSubmitJob from whitespace-separated file. * Dispose of this with edwSubmitJobFreeList(). */ struct edwSubmitJob *edwSubmitJobLoadAllByChar(char *fileName, char chopper); /* Load all edwSubmitJob from chopper separated file. * Dispose of this with edwSubmitJobFreeList(). */ #define edwSubmitJobLoadAllByTab(a) edwSubmitJobLoadAllByChar(a, '\t'); /* Load all edwSubmitJob from tab separated file. * Dispose of this with edwSubmitJobFreeList(). */ struct edwSubmitJob *edwSubmitJobCommaIn(char **pS, struct edwSubmitJob *ret); /* Create a edwSubmitJob out of a comma separated string. * This will fill in ret if non-null, otherwise will * return a new edwSubmitJob */ void edwSubmitJobFree(struct edwSubmitJob **pEl); /* Free a single dynamically allocated edwSubmitJob such as created * with edwSubmitJobLoad(). */ void edwSubmitJobFreeList(struct edwSubmitJob **pList); /* Free a list of dynamically allocated edwSubmitJob's */ void edwSubmitJobOutput(struct edwSubmitJob *el, FILE *f, char sep, char lastSep); /* Print out edwSubmitJob. Separate fields with sep. Follow last field with lastSep. */ #define edwSubmitJobTabOut(el,f) edwSubmitJobOutput(el,f,'\t','\n'); /* Print out edwSubmitJob as a line in a tab-separated file. */ #define edwSubmitJobCommaOut(el,f) edwSubmitJobOutput(el,f,',',','); /* Print out edwSubmitJob as a comma separated list including final comma. */ /* -------------------------------- End autoSql Generated Code -------------------------------- */ #endif /* ENCODEDATAWAREHOUSE_H */