14a7e9de4b1e9c2cc6fd6c1b4912c147afd05064 braney Fri Mar 5 10:56:27 2021 -0800 fix up usage message to make it clearer that bigBeds are allowed and that the tool does a bitwise AND diff --git src/hg/featureBits/featureBits.c src/hg/featureBits/featureBits.c index abd1e84..a6a260a 100644 --- src/hg/featureBits/featureBits.c +++ src/hg/featureBits/featureBits.c @@ -64,41 +64,41 @@ boolean countBlocks = FALSE; /* Count blocks in bed12 rather than extent. */ /* to process chroms without constantly looking up in chromInfo, create * this list of them from the chromInfo once. */ static struct chromInfo *chromInfoList = NULL; static struct hash *gapHash = NULL; void usage() /* Explain usage and exit. */ { errAbort( "featureBits - Correlate tables via bitmap projections. \n" "usage:\n" " featureBits database table(s)\n" - "This will return the number of bits in all the tables anded together\n" + "This will return the number of bits in all the tables bitwise ANDed together\n" "Pipe warning: output goes to stderr.\n" "Options:\n" " -bed=output.bed Put intersection into bed format. Can use stdout.\n" " -fa=output.fa Put sequence in intersection into .fa file\n" " -faMerge For fa output merge overlapping features.\n" " -minSize=N Minimum size to output (default 1)\n" " -chrom=chrN Restrict to one chromosome\n" " -chromSize=sizefile Read chrom sizes from file instead of database. \n" " (chromInfo three column format)\n" - " -or Or tables together instead of anding them\n" + " -or Bitwise OR tables together instead of ANDing them.\n" " -not Output negation of resulting bit set.\n" " -countGaps Count gaps in denominator\n" " -countBlocks Count blocks in bed12 files rather than entire extent.\n" " -noRandom Don't include _random (or Un) chromosomes\n" " -noHap Don't include _hap|_alt chromosomes\n" " -primaryChroms Primary assembly (chroms without '_' in name)\n" " -dots=N Output dot every N chroms (scaffolds) processed\n" " -minFeatureSize=n Don't include bits of the track that are smaller than\n" " minFeatureSize, useful for differentiating between\n" " alignment gaps and introns.\n" " -bin=output.bin Put bin counts in output file\n" " -binSize=N Bin size for generating counts in bin file (default 500000)\n" " -binOverlap=N Bin overlap for generating counts in bin file (default 250000)\n" " -bedRegionIn=input.bed Read in a bed file for bin counts in specific regions \n" " and write to bedRegionsOut\n" @@ -117,30 +117,32 @@ " :exon:N Break into exons and add N to each end of each exon\n" " :cds Break into coding exons\n" " :intron:N Break into introns, remove N from each end\n" " :utr5, :utr3 Break into 5' or 3' UTRs\n" " :upstream:N Consider the region of N bases before region\n" " :end:N Consider the region of N bases after region\n" " :score:N Consider records with score >= N \n" " :upstreamAll:N Like upstream, but doesn't filter out genes that \n" " have txStart==cdsStart or txEnd==cdsEnd\n" " :endAll:N Like end, but doesn't filter out genes that \n" " have txStart==cdsStart or txEnd==cdsEnd\n" "The tables can be bed, psl, or chain files, or a directory full of\n" "such files as well as actual database tables. To count the bits\n" "used in dir/chrN_something*.bed you'd do:\n" " featureBits database dir/_something.bed\n" + "File types supported are BED, bigBed, PSL, and chain. The suffix of the file \n" + "is used to determine the type and MUST be .bed, .bb, .psl, or .chain respectively.\n" "NB: by default, featureBits omits gap regions from its calculation of the total\n" "number of bases. This requires connecting to a database server using credentials\n" "from a .hg.conf file (or similar). If such a connection is not available, you will\n" "need to specify -countGaps (which skips the database connection) in addition to\n" "providing all tables as files or directories.\n" ); } static struct chromInfo *fbCreateChromInfoList(char *name, char *database) /* Load up all chromosome infos. */ { struct sqlConnection *conn = sqlConnect(database); struct sqlResult *sr = NULL; char **row; int loaded=0;