Skip to content

Commit

Permalink
New features for RNASeq data
Browse files Browse the repository at this point in the history
  • Loading branch information
@r78v10a07
r78v10a07 committed Jul 18, 2019
1 parent 4130f05 commit 0384b06
Show file tree
Hide file tree
Showing 3 changed files with 28 additions and 14 deletions.
4 changes: 2 additions & 2 deletions src/BAMcoverage.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ int ReadStrand(bam1_t *read, int paired_end) {
if (read->core.flag & (BAM_FREVERSE)) {
return -1;
} else
return 11;
return 1;
}
}

Expand Down Expand Up @@ -920,7 +920,7 @@ void MultiGenomeBaseCoverage(CMDINPUT *cmd, CHROMOSOMES *chr) {
bamcurr = bamcurr->next;

if(cmd->strandsplit)
cmd->strand = -1;
cmd->strand = 1;
}

DestroyThreadStruct(&threadStruct, cmd->threads);
Expand Down
28 changes: 20 additions & 8 deletions src/Inputs.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ void PrintScaleMessage(char *pname) {
ptr = ptr ? ptr + 1 : (char *) pname;

fprintf(stderr, "\nScale one or multiple BAM files\n");
fprintf(stderr, "Version: %s\n", "v1.0");
fprintf(stderr, "Version: %s\n", "v0.0.5");
fprintf(stderr, "\nUsage: %s scale [OPTIONS] --bam <BAM_1> (--bam <BAM_2> ... --bam <BAM_N>)\n", ptr);
fprintf(stderr, "\nOutput: Coverage tracks in BigWig format (un-scaled, scaled, genome scaled)\n");
fprintf(stderr, "\nRequired options:\n");
Expand All @@ -159,20 +159,32 @@ void PrintScaleMessage(char *pname) {
fprintf(stderr, "\t\t\t\t example in case of three input BAM files: 0.643,0.45667,1.3.\n");

fprintf(stderr, "\n\t--operation|-r <str>\tOperation to perform when scaling samples. Default: %s\n", cmd->operation);
fprintf(stderr, "\t\t\t\tOptions are: \n\t\t\t\t 1) scaled: output scaled tracks.\n\t\t\t\t 2) unscaled: do not scale files in any way.\n\t\t\t\t 2) log2: log2 transform against first BAM file.\n");
fprintf(stderr, "\t\t\t\t 3) ratio: coverage ratio against first BAM file.\n\t\t\t\t 4) subtract: subtract coverage against first BAM file.\n");
fprintf(stderr, "\t\t\t\tOptions are: \n");
fprintf(stderr, "\t\t\t\t 1) scaled: output scaled tracks\n");
fprintf(stderr, "\t\t\t\t 2) unscaled: do not scale files in any way\n");
fprintf(stderr, "\t\t\t\t 3) log2: log2 transform against first BAM file\n");
fprintf(stderr, "\t\t\t\t 4) ratio: coverage ratio against first BAM file.\n\t\t\t\t 5) subtract: subtract coverage against first BAM file.\n");
fprintf(stderr, "\t\t\t\t 5) rfd: OK-seq RFD calculation\n");
fprintf(stderr, "\t\t\t\t 6) endseq: strand-specific coverages\n");
fprintf(stderr, "\t\t\t\t 6) endseqr: strand-specific coverages (reverse strand score is negative)\n");
fprintf(stderr, "\t\t\t\t 7) reptime: replication timing mode for two BAM files (binsize: 100bp, smoothen: 500 bins)\n");
fprintf(stderr, "\t\t\t\t 7) endseqr: strand-specific coverages (reverse strand score is negative)\n");
fprintf(stderr, "\t\t\t\t 8) reptime: replication timing mode for two BAM files (binsize: 100bp, smoothen: 500 bins)\n");
fprintf(stderr, "\t\t\t\t 9) rna: coverage of RNA-seq file (one file at a time)\n");
fprintf(stderr, "\t\t\t\t 10) strandrna: stranded coverage of RNA-seq file (one file at a time)\n");
fprintf(stderr, "\t\t\t\t 11) strandrnaR: stranded coverage of RNA-seq file (reverse is negative, one file at a time)\n");

fprintf(stderr, "\n\t\t\t\tShort description of settings:\n");
fprintf(stderr, "\t\t\t\tendseq: generates scaled coverage tracks of positive/negative strands,\n");
fprintf(stderr, "\t\t\t\t\tand the log2 ratios\n");
fprintf(stderr, "\n\t\t\t\tendseqr: generates scaled coverage tracks of positive/negative strands,\n");
fprintf(stderr, "\t\t\t\t\tthe negative strand coverage will be negative, and the log2 ratios are calculated\n");
fprintf(stderr, "\n\t\t\t\treptime: generates scaled coverage tracks and log2 ratios of two BAM files,\n");
fprintf(stderr, "\t\t\t\t\tsetting the binsize to 100bp and smoothening smoothen to 500 bins\n");

fprintf(stderr, "\n\t\t\t\trna: coverage of RNA-seq, useful for accurate coverages at exon-intron boundaries\n");
fprintf(stderr, "\n\t\t\t\tstrandrna: stranded coverage of RNA-seq, useful for accurate coverages at exon-intron boundaries,\n");
fprintf(stderr, "\t\t\t\t\tcreating separate tracks for forward and reverse strand\n");
fprintf(stderr, "\n\t\t\t\tstrandrnaR: stranded coverage of RNA-seq, useful for accurate coverages at exon-intron boundaries,\n");
fprintf(stderr, "\t\t\t\t\tcreating separate tracks for forward and reverse strand, reverse strand is negated\n");

fprintf(stderr, "\n\t-S <flag>\t\tOutput strand-specific normalized tracks. One BAM file can be specified only\n");

fprintf(stderr, "\n\t--binsize|-z <int>\tSize of bins for output bigWig/bedgraph generation (default: %d)\n", cmd->binSize);
Expand Down Expand Up @@ -615,7 +627,7 @@ CMDINPUT *ScaleParser(int argc, char **argv) {
cmd->no_of_samples++;
}

cmd->strand = 1;
cmd->strand = -1;
}
}

Expand Down Expand Up @@ -778,7 +790,7 @@ void PrintMultiCovMessage(char *pname) {
ptr = ptr ? ptr + 1 : (char *) pname;

fprintf(stderr, "\nCalculate coverage of BED coordinates in BAM file(s)\n");
fprintf(stderr, "Version: %s\n", "v1.0");
fprintf(stderr, "Version: %s\n", "v0.0.5");
fprintf(stderr, "\nUsage: %s cov [OPTIONS] --bed <BEDFILE> --bam <BAM_1> (--bam <BAM_2> ... --bam <BAM_N>)\n", ptr);
fprintf(stderr, "\nOutput: Coverage tables (un-normalized, library-size normalized, FPKM and TPM)\n");
fprintf(stderr, "\nRequired options:\n");
Expand Down
10 changes: 6 additions & 4 deletions src/main.c
View file
Original file line number Diff line number Diff line change
Expand Up @@ -318,8 +318,10 @@ void NormalizeBAMS(CMDINPUT *cmd) {
MultiGenomeBaseCoverage(cmd, CHROMhead);

if(cmd->strandsplit == 1 && strcmp(cmd->scale, INPUTS_CUSTOM) != 0) {
cmd->bamfiles->base_coverage = cmd->bamfiles->base_coverage + cmd->bamfiles->next->base_coverage;
cmd->bamfiles->next->base_coverage = cmd->bamfiles->base_coverage;
if(strcmp(cmd->operation, INPUTS_RSTRRNA) == 0 || strcmp(cmd->operation, INPUTS_STRRNA) == 0) {
cmd->bamfiles->base_coverage = cmd->bamfiles->base_coverage + cmd->bamfiles->next->base_coverage;
cmd->bamfiles->next->base_coverage = cmd->bamfiles->base_coverage;
}
}

if(strcmp(cmd->scale, INPUTS_CUSTOM) != 0)
Expand Down Expand Up @@ -363,14 +365,14 @@ void NormalizeBAMS(CMDINPUT *cmd) {

curr = cmd->bamfiles;
if(cmd->strandsplit == 1)
cmd->strand = 1;
cmd->strand = -1;

while (curr != NULL) {
PrintScaledBigWig(cmd, curr, NULL);
curr = curr->next;

if(cmd->strandsplit == 1)
cmd->strand = -1;
cmd->strand = 1;
}

if (strcmp(cmd->operation, "scaled") != 0 && strcmp(cmd->operation, "unscaled") != 0) {
Expand Down

0 comments on commit 0384b06

Please sign in to comment.