git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@95415 bc3139a8-67e5-0310-9ffc-ced21a209358
Herve Pages authored on 13/10/2014 19:02:34 | 1 | 1 |
new file mode 100644 |
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+/* |
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+ * fq_traverse.h |
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+ * |
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+ * Created on: 12.10.2013 |
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+ * Author: wolfgang |
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+ */ |
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+ |
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+#ifndef FQ_TRAVERSE_H_ |
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+#define FQ_TRAVERSE_H_ |
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+ |
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+#include "stat_defs.h" |
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+#include "dna_astream.h" |
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+ |
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+/////////////////////////////////////////////////////////////////////////////////////////////////// |
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+// |
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+// Fastq traverse: |
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+// Contains dna_astream which is traversed. |
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| 18 |
+// The <seqname> following '+' is optional, |
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+// but if it appears right after '+', it should be identical to the <seqname> following '@'. |
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+// The length of <seq> is identical the length of <qual>. Each character in <qual> represents the phred quality of the corresponding nucleotide in <seq>. |
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+ |
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+// |
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+/////////////////////////////////////////////////////////////////////////////////////////////////// |
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+ |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+// |
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+// Definition of static constants |
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+// |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+static const unsigned long faq_array_size =0xFFFFFF; // char array capacity |
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+ |
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+static const char faq_char_sqDelim ='@'; // Fastq sequence delimiter |
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+static const char faq_char_qlDelim ='+'; // Fastq quality delimiter |
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+static const char faq_char_lf ='\n'; // Line feed |
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+static const char faq_char_eos ='\0'; // End of string |
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+ |
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+static const int faq_ok =0; |
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+static const int faq_empty =1; |
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+static const int faq_newSeq =4; |
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+ |
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+ |
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+typedef struct fastq_traverse |
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+{
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+ daStream *das; |
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+ |
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+ int state; |
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+ unsigned nSeq; // Number of sequences |
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+ unsigned nFill; // Number of fill operations. |
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+ unsigned nProcFull; // Number of times where proc array was filled up. |
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+ |
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+ unsigned minSeqLen; |
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+ unsigned maxSeqLen; |
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+ |
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+ unsigned lastSeqLen; |
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+ unsigned nUneqLeqLen; |
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+ |
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+} fqTraverse; |
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+ |
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+ |
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+int faqEmpty(fqTraverse* faq) { return dasEmpty(faq->das); }
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+int faqIsOpen(fqTraverse* faq) { return dasIsOpen(faq->das); }
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+int faqIsEof(fqTraverse* faq) { return dasIsEof(faq->das); }
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+ |
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+void faq_destroy(fqTraverse *faq) |
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+{
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+ if(faq) |
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+ {
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+ das_destroy(faq->das); |
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+ free(faq); |
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+ } |
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+} |
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+ |
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+ |
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+fqTraverse * faq_init(const char* filename, unsigned mode) |
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+{
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+ fqTraverse * faq=(fqTraverse*)calloc(sizeof(fqTraverse),1); |
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+ |
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+ if(!faq) |
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+ return 0; |
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+ |
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+ faq->das=das_init(filename,mode,faq_array_size); |
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+ |
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+ if(!faq->das) |
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+ {
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+ //printf("[faq_init] das_init returned 0!\n");
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+ free(faq); |
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+ return 0; |
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+ } |
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+ // initialize with large value |
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+ --faq->minSeqLen; |
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+ |
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+ // Returns memory initialized object. |
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+ // File may be closed. |
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+ // File may be empty. |
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+ // Stream is not yet initialized. |
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+ return faq; |
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+} |
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+ |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+// Check-Fill: Checks for empty rfc (frs==0) and eventually fills das. |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+int faqCheckFill(fqTraverse *faq) |
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+{
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+ //printf("[faqCheckFill].\n");
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+ if(dasEmpty(faq->das)) |
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+ {
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+ //printf("[faqCheckFill] ->das_fill\n");
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+ if(das_fill(faq->das)) |
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+ {
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+ ++(faq->nFill); |
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+ faq->state|=faq_empty; |
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+ return faq->state; |
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+ } |
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+ faq->state&=(~faq_empty); |
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+ } |
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+ return faq_ok; |
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+} |
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+ |
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+int faqCheckCapFill(fqTraverse *faq,int capacity) |
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+{
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+ daStream *das=faq->das; |
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+ if(das->r_end-das->r_iter<capacity) |
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+ {
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+ if(das_fill(das)) |
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+ {
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+ ++(faq->nFill); |
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+ faq->state|=faq_empty; |
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+ return faq->state; |
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+ } |
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+ faq->state&=(~faq_empty); |
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+ } |
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+ return faq_ok; |
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+} |
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+ |
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+ |
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+ |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+// Check section (Must be placed beforehand skip-routines) |
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+// faq_checkNewLine |
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+// faq_checkSeqHeader |
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+// faq_checkComment |
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+// faq_checkN |
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+// faq_check_nuc |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+ |
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+ |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+// Skip section (Do not reorder...) |
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+// faq_checkSkipNewLine |
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+// faq_skipLine |
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+// faq_skipComment |
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+// faq_skipN |
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+// + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+static inline int faq_checkSkipNewLine(fqTraverse *faq) |
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+{
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+ // Skips LF ('\n') character and
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+ // eventually tries to fill array |
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+ |
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+ //printf("[CheckNewLine].\n");
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+ if(*faq->das->r_iter==faq_char_lf) |
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+ {
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+ if(faqCheckCapFill(faq,2)) |
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+ return faq->state; |
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+ // Eat newline |
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+ ++faq->das->r_iter; |
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+ return faq_ok; |
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+ } |
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+ return faq->state; |
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+} |
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+ |
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+static inline int faq_skipLastNewLine(fqTraverse *faq) |
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+{
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+ daStream *das=faq->das; |
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+ if((*faq->das->r_iter==faq_char_lf) & (das->dnaf->state==dfs_file_closed)) |
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+ {
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+ ++das->r_iter; |
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+ return faq_ok; |
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+ } |
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+ return faq_empty; |
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+} |
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+ |
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+ |
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+static inline int faq_skipLine(fqTraverse *faq) |
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+{
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+ // Traverses until first position of next line |
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+ // and eventually tries to refill array |
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+ daStream *das=faq->das; |
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+ while(*das->r_iter!=faq_char_lf) |
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+ {
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+ ++das->r_iter; |
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+ if(faqCheckFill(faq)) |
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+ return faq->state; |
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+ } |
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+ ++das->r_iter; |
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+ |
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+ if(faqCheckFill(faq)) |
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+ return faq->state; |
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+ |
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+ return faq_ok; |
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+} |
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+ |
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+int faq_procNuc(fqTraverse *faq) |
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+{
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+ // + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ // Copies one line of continuous Nucleotide sequence |
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+ // from: input fastq stream (rfc array) |
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+ // to : output nucleotide stream (pos array) |
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+ // |
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+ // Copy procedure ends when: |
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+ // A) A non nucleotide is found. |
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+ // B) Quality header ('+') is found.
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+ // C) rfc array runs empty. |
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+ // D) pos array is filled up. |
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+ // |
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+ // Tries to recover when end of rfc-array is reached. |
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+ // Copying always starts at begin of nuc array |
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+ // |
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+ // Returns fat_ok (=0) when *NO* output is created. |
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+ // |
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+ // Allows 'if(fat_procNuc) => process output' |
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+ // testing. |
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+ // + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+ daStream *das=faq->das; |
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+ unsigned seqLen=0; |
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+ |
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+ //printf("[faq pNuc] start: '%s'\n",das->r_iter);
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+ |
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+ // Empty array must be prevented here |
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+ if(faqCheckFill(faq)) |
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+ {
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ |
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+ |
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+ if(*faq->das->r_iter==faq_char_sqDelim) |
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+ {
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+ // Skip header line |
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+ if(faq_skipLine(faq)) |
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+ {
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ |
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+ // Goto begin of pos array. |
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+ das->p_iter=das->pos; |
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+ //printf("[faq pNuc] while: '%s'\n",das->r_iter);
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+ ++faq->nSeq; |
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+ |
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+ while(!((ACGT[(unsigned)*das->r_iter]==zval) || *das->r_iter==faq_char_qlDelim ) ) |
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+ {
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+ |
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+ *das->p_iter=*das->r_iter; |
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+ ++das->r_iter; |
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+ ++das->p_iter; |
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+ ++seqLen; |
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+ //printf("[faq pNuc] fill: '%s'\n",das->r_iter);
|
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+ // Two recoverable conditions: |
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+ if(faqCheckFill(faq)) |
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+ {
|
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ if(faq_checkSkipNewLine(faq)) |
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+ {
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ if(dasProcEmpty(das)) |
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+ {
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+ ++faq->nProcFull; |
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ } |
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+ // Add string termination |
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+ if(!dasProcEmpty(das)) |
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+ {
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+ das->npPos=(das->p_iter-das->pos); |
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+ *das->p_iter=faq_char_eos; |
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+ } |
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+ } |
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+} |
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+ |
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+int faq_procPhred(fqTraverse *faq) |
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+{
|
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+ // + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ // Copies one line of Phred characters |
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+ // from: input fastq stream (rfc array) |
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+ // to : output nucleotide stream (pos array) |
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+ // |
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+ // Copy procedure ends when: |
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+ // A) Sequence header ('@') is found.
|
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+ // B) rfc array runs empty. |
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+ // C) pos array is filled up. |
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+ // |
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+ // Tries to recover when end of rfc-array is reached. |
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+ // Copying always starts at begin of pos array. |
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+ // |
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+ // Returns fat_ok (=0) when *NO* output is created. |
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+ // |
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+ // Allows 'if(fat_procNuc) => process output' |
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+ // testing. |
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+ // + + + + + + + + + + + + + + + + + + + + + + + + + + // |
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+ |
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+ daStream *das=faq->das; |
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+ unsigned seqLen=0; |
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+ |
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+ // Empty array must be prevented here |
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+ if(faqCheckFill(faq)) |
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+ {
|
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ |
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+ //printf("[faq_Phred] start: '%s'\n",das->r_iter);
|
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+ if(*faq->das->r_iter==faq_char_qlDelim) |
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+ {
|
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+ // Skip header line |
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| 327 |
+ if(faq_skipLine(faq)) |
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+ {
|
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+ faq->lastSeqLen=seqLen; |
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+ return seqLen; |
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+ } |
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+ if(faqCheckFill(faq)) |
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+ return 0; |
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+ |
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+ // Goto begin of pos array. |
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+ das->p_iter=das->pos; |
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+ // Copy until new seq header is found |
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+ |
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+ //printf("[faq_Phred] while: '%s'\n",das->r_iter);
|
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+ while(!(*das->r_iter==faq_char_sqDelim)) |
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+ {
|
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+ *das->p_iter=*das->r_iter; |
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+ ++das->r_iter; |
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+ ++das->p_iter; |
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+ ++seqLen; |
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+ |
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+ //printf("[faq Phred] while: '%s'\tr_iter:%li\n",das->r_iter,das->r_end-das->r_iter);
|
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+ // Two recoverable conditions: |
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| 349 |
+ if(faqCheckFill(faq)) |
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+ {
|
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| 351 |
+ //printf("[faq_Phred] checkFill: %u\n",faq->nFill);
|
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| 352 |
+ if(seqLen!=faq->lastSeqLen) |
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+ ++faq->nUneqLeqLen; |
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+ return seqLen; |
|
| 355 |
+ } |
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| 356 |
+ if(faq_checkSkipNewLine(faq)) |
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+ {
|
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| 358 |
+ if(seqLen!=faq->lastSeqLen) |
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| 359 |
+ ++faq->nUneqLeqLen; |
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| 360 |
+ return seqLen; |
|
| 361 |
+ } |
|
| 362 |
+ if(dasProcEmpty(das)) |
|
| 363 |
+ {
|
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| 364 |
+ ++faq->nProcFull; |
|
| 365 |
+ if(seqLen!=faq->lastSeqLen) |
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| 366 |
+ ++faq->nUneqLeqLen; |
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| 367 |
+ return seqLen; |
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| 368 |
+ } |
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| 369 |
+ } |
|
| 370 |
+ // Add string termination |
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| 371 |
+ if(!dasProcEmpty(das)) |
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| 372 |
+ {
|
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| 373 |
+ das->npPos=(das->p_iter-das->pos); |
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| 374 |
+ *das->p_iter=faq_char_eos; |
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| 375 |
+ } |
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| 376 |
+ |
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| 377 |
+ if(seqLen!=faq->lastSeqLen) |
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| 378 |
+ ++faq->nUneqLeqLen; |
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| 379 |
+ } |
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+ return seqLen; |
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| 381 |
+} |
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+ |
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+ |
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| 384 |
+#endif /* FQ_TRAVERSE_H_ */ |