[med-svn] [soapsnp] 07/09: New upstream version 1.03
Andreas Tille
tille at debian.org
Thu Dec 28 07:17:48 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository soapsnp.
commit 2551b17dac9a39ee457db8b709b1922fa48f8f2d
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 28 08:16:33 2017 +0100
New upstream version 1.03
---
.cproject | 943 ++++++++++++++++++++++++++++++++++++++++++
.main.cc.swp | Bin 0 -> 16384 bytes
.project | 82 ++++
.soap_snp.h.swp | Bin 0 -> 4096 bytes
COPYING | 674 ++++++++++++++++++++++++++++++
call_genotype.cc | 583 ++++++++++++++++++++++++++
chromosome.cc | 220 ++++++++++
debian/README.Debian | 10 -
debian/changelog | 9 -
debian/compat | 1 -
debian/control | 37 --
debian/copyright | 28 --
debian/docs | 1 -
debian/patches/Makefile.patch | 12 -
debian/patches/series | 1 -
debian/rules | 11 -
debian/source/format | 1 -
debian/upstream/metadata | 14 -
debian/watch | 2 -
main.cc | 332 +++++++++++++++
makefile | 18 +
matrix.cc | 219 ++++++++++
normal_dis.cc | 24 ++
prior.cc | 97 +++++
rank_sum.cc | 128 ++++++
readme | 139 +++++++
release | 5 +
soap_snp.h | 326 +++++++++++++++
28 files changed, 3790 insertions(+), 127 deletions(-)
diff --git a/.cproject b/.cproject
new file mode 100644
index 0000000..de7f5ff
--- /dev/null
+++ b/.cproject
@@ -0,0 +1,943 @@
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+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.make.core.GCCStandardMakePerFileProfile">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="makefileGenerator">
+<runAction arguments="-f ${project_name}_scd.mk" command="make" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfile">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileCPP">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCManagedMakePerProjectProfileC">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfile">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/${specs_file}" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileCPP">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.cpp" command="g++" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+<profile id="org.eclipse.cdt.managedbuilder.core.GCCWinManagedMakePerProjectProfileC">
+<buildOutputProvider>
+<openAction enabled="true" filePath=""/>
+<parser enabled="true"/>
+</buildOutputProvider>
+<scannerInfoProvider id="specsFile">
+<runAction arguments="-E -P -v -dD ${plugin_state_location}/specs.c" command="gcc" useDefault="true"/>
+<parser enabled="true"/>
+</scannerInfoProvider>
+</profile>
+</scannerConfigBuildInfo>
+</storageModule>
+</cconfiguration>
+</storageModule>
+<storageModule moduleId="cdtBuildSystem" version="4.0.0">
+<project id="SOAPsnpZ.cdt.managedbuild.target.macosx.exe.1112108921" name="Executable" projectType="cdt.managedbuild.target.macosx.exe"/>
+</storageModule>
+</cproject>
diff --git a/.main.cc.swp b/.main.cc.swp
new file mode 100644
index 0000000..9dfdec0
Binary files /dev/null and b/.main.cc.swp differ
diff --git a/.project b/.project
new file mode 100644
index 0000000..4d81a5f
--- /dev/null
+++ b/.project
@@ -0,0 +1,82 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>SOAPsnpZ</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.cdt.managedbuilder.core.genmakebuilder</name>
+ <triggers>clean,full,incremental,</triggers>
+ <arguments>
+ <dictionary>
+ <key>?name?</key>
+ <value></value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.append_environment</key>
+ <value>true</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.autoBuildTarget</key>
+ <value>all</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.buildArguments</key>
+ <value></value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.buildCommand</key>
+ <value>make</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.buildLocation</key>
+ <value>${workspace_loc:/SOAPsnpZ/Debug}</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.cleanBuildTarget</key>
+ <value>clean</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.contents</key>
+ <value>org.eclipse.cdt.make.core.activeConfigSettings</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.enableAutoBuild</key>
+ <value>false</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.enableCleanBuild</key>
+ <value>true</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.enableFullBuild</key>
+ <value>true</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.fullBuildTarget</key>
+ <value>all</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.stopOnError</key>
+ <value>true</value>
+ </dictionary>
+ <dictionary>
+ <key>org.eclipse.cdt.make.core.useDefaultBuildCmd</key>
+ <value>true</value>
+ </dictionary>
+ </arguments>
+ </buildCommand>
+ <buildCommand>
+ <name>org.eclipse.cdt.managedbuilder.core.ScannerConfigBuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.cdt.core.cnature</nature>
+ <nature>org.eclipse.cdt.managedbuilder.core.ScannerConfigNature</nature>
+ <nature>org.eclipse.cdt.core.ccnature</nature>
+ <nature>org.eclipse.cdt.managedbuilder.core.managedBuildNature</nature>
+ </natures>
+</projectDescription>
diff --git a/.soap_snp.h.swp b/.soap_snp.h.swp
new file mode 100644
index 0000000..42989e0
Binary files /dev/null and b/.soap_snp.h.swp differ
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
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+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
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+ When we speak of free software, we are referring to freedom, not
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+ Developers that use the GNU GPL protect your rights with two steps:
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diff --git a/call_genotype.cc b/call_genotype.cc
new file mode 100644
index 0000000..3d1fddb
--- /dev/null
+++ b/call_genotype.cc
@@ -0,0 +1,583 @@
+#include "soap_snp.h"
+#include <cassert>
+
+int Call_win::initialize(ubit64_t start) {
+ std::string::size_type i;
+ for(i=0; i != read_len + win_size ; i++) {
+ sites[i].pos = i+start;
+ }
+ return 1;
+}
+
+int Call_win::deep_init(ubit64_t start) {
+ int i;
+ for(i=0; i != read_len + win_size ; i++) {
+ sites[i].pos = i+start;
+ sites[i].ori = 0xFF;
+ sites[i].depth = 0;
+ sites[i].repeat_time = 0;
+ sites[i].dep_uni = 0;
+ memset(sites[i].count_uni,0,sizeof(int)*4);
+ memset(sites[i].q_sum,0,sizeof(int)*4);
+ memset(sites[i].base_info,0,sizeof(small_int)*4*2*64*256);
+ memset(sites[i].count_all,0,sizeof(int)*4);
+ }
+ return 1;
+}
+
+int Call_win::recycle() {
+ std::string::size_type i;
+ for(i=0; i != read_len ; i++) {
+ sites[i].pos = sites[i+win_size].pos;
+ sites[i].ori = sites[i+win_size].ori;
+ sites[i].depth = sites[i+win_size].depth;
+ sites[i].repeat_time = sites[i+win_size].repeat_time;
+ sites[i].dep_uni = sites[i+win_size].dep_uni;
+ memcpy(sites[i].base_info, sites[i+win_size].base_info, sizeof(small_int)*4*2*64*256); // 4 types of bases, 2 strands, max quality score is 64, and max read length 256
+ memcpy(sites[i].count_uni, sites[i+win_size].count_uni, sizeof(int)*4);
+ memcpy(sites[i].q_sum, sites[i+win_size].q_sum, sizeof(int)*4);
+ memcpy(sites[i].count_all, sites[i+win_size].count_all, sizeof(int)*4);
+ }
+ for(i=read_len; i != read_len+win_size; i++) {
+ sites[i].ori = 0xFF;
+ sites[i].pos = sites[i-1].pos+1;
+ sites[i].depth = 0;
+ sites[i].repeat_time = 0;
+ sites[i].dep_uni = 0;
+ memset(sites[i].count_uni,0,sizeof(int)*4);
+ memset(sites[i].q_sum,0,sizeof(int)*4);
+ memset(sites[i].base_info,0,sizeof(small_int)*4*2*64*256);
+ memset(sites[i].count_all,0,sizeof(int)*4);
+ }
+ return 1;
+}
+
+
+int Call_win::call_cns(Chr_name call_name, Chr_info* call_chr, ubit64_t call_length, Prob_matrix * mat, Parameter * para, std::ofstream & consensus, std::ofstream & baseinfo) {
+ std::string::size_type coord;
+ small_int k;
+ ubit64_t o_base, strand;
+ char allele1, allele2, genotype, type, type1/*best genotype*/, type2/*suboptimal genotype*/, base1, base2, base3;
+ int i, q_score, q_adjusted, qual1, qual2, qual3, q_cns, all_count1, all_count2, all_count3;
+ int global_dep_count, *pcr_dep_count;
+ pcr_dep_count = new int [para->read_length*2];
+ double rank_sum_test_value, binomial_test_value;
+ bool is_out;
+ double * real_p_prior = new double [16];
+ double * likelihoods = new double [10];
+ memset(likelihoods, 0, sizeof(double)*10);
+ //std::cerr<<"Call length="<<call_length<<endl;
+ for(std::string::size_type j=0; j != call_length; j++){
+ //cerr<<sites[j].pos<<endl;
+ if(para->region_only) {
+ if (NULL== call_chr->get_region() ) {
+ break;
+ }
+ else if (! call_chr->is_in_region(sites[j].pos)) {
+ continue;
+ }
+ else {
+ ;
+ }
+ }
+ sites[j].ori = (call_chr->get_bin_base(sites[j].pos))&0xF;
+ if( ((sites[j].ori&4) !=0)/*an N*/ && sites[j].depth == 0) {
+ // CNS text format:
+ // ChrID\tPos\tRef\tCns\tQual\tBase1\tAvgQ1\tCountUni1\tCountAll1\tBase2\tAvgQ2\tCountUni2\tCountAll2\tDepth\tRank_sum\tCopyNum\tSNPstauts\n"
+ if(!para->glf_format && ! para->is_snp_only) {
+ consensus<<call_name<<'\t'<<(sites[j].pos+1)<<"\tN\tN\t0\tN\t0\t0\t0\tN\t0\t0\t0\t0\t1.000\t255.000\t0"<<endl;
+ }
+ else if (para->glf_format) {
+ memset(likelihoods, 0, sizeof(double)*10);
+ consensus.write(reinterpret_cast<char*>(likelihoods), sizeof(double)*10);
+ consensus<<flush;
+ if(!consensus.good()) {
+ cerr<<"Broken ofstream after writting Position "<<(sites[j].pos+1)<<" at "<<call_name<<endl;
+ exit(255);
+ }
+ baseinfo<<call_name<<'\t'<<(sites[j].pos+1)<<"\tN\tN\t0\tN\t0\t0\t0\tN\t0\t0\t0\t0\t1.000\t255.000\t0"<<endl;
+ }
+ else {
+ ;
+ }
+ continue;
+ }
+ base1 = 0, base2 = 0, base3 = 0;
+ qual1 = -1, qual2= -2, qual3 = -3;
+ all_count1 = 0, all_count2 =0, all_count3 =0;
+ if(sites[j].dep_uni) {
+ // This position is uniquely covered by at least one nucleotide
+ for(i=0;i!=4;i++) {
+ // i is four kind of alleles
+ if(sites[j].q_sum[i] >= qual1) {
+ base3 = base2;
+ qual3 = qual2;
+ base2 = base1;
+ qual2 = qual1;
+ base1 = i;
+ qual1 = sites[j].q_sum[i];
+ }
+ else if (sites[j].q_sum[i]>=qual2) {
+ base3 = base2;
+ qual3 = qual2;
+ base2 = i;
+ qual2 = sites[j].q_sum[i];
+ }
+ else if (sites[j].q_sum[i]>=qual3) {
+ base3 = i;
+ qual3 = sites[j].q_sum[i];
+ }
+ else {
+ ;
+ }
+ }
+ if(qual1 == 0) {
+ // Adjust the best base so that things won't look ugly if the pos is not covered
+ base1 = (sites[j].ori&7);
+ }
+ else if(qual2 ==0 && base1 != (sites[j].ori&7)) {
+ base2 = (sites[j].ori&7);
+ }
+ else {
+ ;
+ }
+ }
+ else {
+ // This position is covered by all repeats
+ for(i=0;i!=4;i++) {
+ if(sites[j].count_all[i] >= all_count1) {
+ base3 = base2;
+ all_count3 = all_count2;
+ base2 = base1;
+ all_count2 = all_count1;
+ base1 = i;
+ all_count1 = sites[j].count_all[i];
+ }
+ else if (sites[j].count_all[i]>=all_count2) {
+ base3 = base2;
+ all_count3 = all_count2;
+ base2 = i;
+ all_count2 = sites[j].count_all[i];
+ }
+ else if (sites[j].count_all[i]>=all_count3) {
+ base3 = i;
+ all_count3 = sites[j].count_all[i];
+ }
+ else {
+ ;
+ }
+ }
+ if(all_count1 ==0) {
+ base1 = (sites[j].ori&7);
+ }
+ else if(all_count2 ==0 && base1 != (sites[j].ori&7)) {
+ base2 = (sites[j].ori&7);
+ }
+ else {
+ ;
+ }
+ }
+ // Calculate likelihood
+ for(genotype=0;genotype!=16;genotype++){
+ mat->type_likely[genotype] = 0.0;
+ }
+ for(o_base=0;o_base!=4;o_base++) {
+ //cerr<<o_base<<endl;
+ if(sites[j].count_uni[o_base]==0) {continue;}
+ global_dep_count = -1;
+ memset(pcr_dep_count, 0, sizeof(int)*2*para->read_length);
+ for(q_score=para->q_max-para->q_min; q_score != -1; q_score--) {
+ for(coord=0; coord != para->read_length; coord++) {
+ for(strand=0; strand!=2; strand++) {
+ for(k=0; k!=sites[j].base_info[o_base<<15|strand<<14|q_score<<8|coord];k++) {
+ if(pcr_dep_count[strand*para->read_length+coord]==0) {
+ global_dep_count += 1;
+ //if(sites[j].pos == 250948) {
+ // cerr<<'g'<<global_dep_count<<'\t';//fprintf(stderr, "Now:%c\t\t%le\t%le\t%le\n", abbv[allele1<<2|allele2], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele1<<2) | o_base], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele2<<2) | o_base], mat->type_likely[allele1<<2|allele2]);
+ //}
+ }
+ pcr_dep_count[strand*para->read_length+coord] += 1;
+ //if(sites[j].pos == 250948) {
+ // cerr<<'p'<<pcr_dep_count[strand*para->read_length+coord]<<'\t';//fprintf(stderr, "Now:%c\t\t%le\t%le\t%le\n", abbv[allele1<<2|allele2], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele1<<2) | o_base], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele2<<2) | o_base], mat->type_likely[allele1<<2|allele2]);
+ //}
+ q_adjusted = int( pow(10, (log10(q_score) +(pcr_dep_count[strand*para->read_length+coord]-1)*para->pcr_dependency +global_dep_count*para->global_dependency)) +0.5);
+ if(q_adjusted < 1) {
+ q_adjusted = 1;
+ }
+ for(allele1 = 0;allele1 != 4;allele1++ ) {
+ for(allele2 = allele1; allele2 != 4; allele2++) {
+ mat->type_likely[allele1<<2|allele2] += log10(0.5*mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele1<<2) | o_base] +0.5*mat->p_matrix[((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele2<<2) | o_base]);
+ //if(sites[j].pos == 52100) {
+ // cerr<<"Now:"<<abbv[allele1<<2|allele2]<<'\t'<<mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele1<<2) | o_base]<<'\t'<<mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele2<<2) | o_base]<<'\t'<<mat->type_likely[allele1<<2|allele2]<<endl;
+ //}
+ }
+ }
+ //if(sites[j].pos == 250948) {
+ // cerr<<q_score<<'\t'<<q_adjusted<<'\t'<<coord<<'_'<<strand<<'\t'<<"ACTG"[o_base]<<'\t'<<mat->type_likely[0]<<'\t'<<mat->type_likely[5]<<'\t'<<mat->type_likely[10]<<'\t'<<mat->type_likely[15]<<endl;//fprintf(stderr, "Now:%c\t\t%le\t%le\t%le\n", abbv[allele1<<2|allele2], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele1<<2) | o_base], mat->p_matrix[ ((ubit64_t)q_adjusted<<12) | (coord <<4) | (allele2<<2) | o_base], mat->type_likely[allele1<<2|allele2]);
+ //}
+ }
+ }
+ }
+ }
+ }
+
+ if(para->glf_format) {
+ for(int i=0; i!=10; i++) {
+ consensus.write(reinterpret_cast<char*>(&mat->type_likely[glf_type_code[i]]), sizeof(double));
+ }
+ consensus<<flush;
+ if(!consensus.good()) {
+ cerr<<"Broken ofstream after writting Position "<<(sites[j].pos+1)<<" at "<<call_name<<endl;
+ exit(255);
+ }
+ //continue;
+ }
+ // Calculate Posterior Probability
+ memcpy(real_p_prior, &mat->p_prior[((ubit64_t)sites[j].ori&0x7)<<4], sizeof(double)*16);
+ if ( (sites[j].ori & 0x8) && para->refine_mode) {
+ // a dbSNP
+ snp_p_prior_gen(real_p_prior, call_chr->find_snp(sites[j].pos), para, sites[j].ori);
+ }
+ memset(mat->type_prob,0,sizeof(rate_t)*17);
+ type2=type1=16;
+ for (allele1=0; allele1!=4; allele1++) {
+ for (allele2=allele1; allele2!=4; allele2++) {
+ genotype = allele1<<2|allele2;
+ if (para->is_monoploid && allele1 != allele2) {
+ continue;
+ }
+ mat->type_prob[genotype] = mat->type_likely[genotype] + log10(real_p_prior[genotype]) ;
+
+ if (mat->type_prob[genotype] >= mat->type_prob[type1] || type1 == 16) {
+ type2 = type1;
+ type1 = genotype;
+ }
+ else if (mat->type_prob[genotype] >= mat->type_prob[type2] || type2 ==16) {
+ type2 = genotype;
+ }
+ else {
+ ;
+ }
+ }
+ }
+ is_out = true; // Check if the position needs to be output, useful in snp-only mode
+
+ if (para->rank_sum_mode) {
+ rank_sum_test_value = rank_test(sites[j], type1, mat->p_rank, para);
+ }
+ else {
+ rank_sum_test_value = 1.0;
+ }
+ if(rank_sum_test_value==0.0) {
+ // avoid double genotype overflow
+ q_cns = 0;
+ }
+ else {
+ q_cns = (int)(10*(mat->type_prob[type1]-mat->type_prob[type2])+10*log10(rank_sum_test_value));
+ }
+
+ if ( (type1&3) == ((type1>>2)&3)) { // Called Homozygous
+ if (qual1>0 && base1 != (type1&3)) {
+ //Wired: best base is not the consensus!
+ q_cns = 0;
+ }
+ else if (/*qual2>0 &&*/ q_cns > qual1-qual2) {
+ // Should not bigger than this
+ q_cns = qual1-qual2;
+ }
+ else {
+ ;
+ }
+ }
+ else { // Called Heterozygous
+ if(sites[j].q_sum[base1]>0 && sites[j].q_sum[base2]>0 && type1 == (base1<base2 ? (base1<<2|base2):(base2<<2|base1))) {
+ // The best bases are in the heterozygote
+ if (q_cns > qual2-qual3) {
+ q_cns = qual2-qual3;
+ }
+ }
+ else { // Ok, wired things happened
+ q_cns = 0;
+ }
+ }
+ if(q_cns>99) {
+ q_cns = 99;
+ }
+ if (q_cns<0) {
+ q_cns = 0;
+ }
+ if(! para->glf_format) {
+ // ChrID\tPos\tRef\tCns\tQual\tBase1\tAvgQ1\tCountUni1\tCountAll1\tBase2\tAvgQ2\tCountUni2\tCountAll2\tDepth\tRank_sum\tCopyNum\tSNPstauts\n"
+ if(! para->is_snp_only || (abbv[type1] != "ACTGNNNN"[(sites[j].ori&0x7)] && sites[j].depth > 0)) {
+ if(base1<4 && base2<4) {
+ consensus<<call_name<<'\t'<<(sites[j].pos+1)<<'\t'<<("ACTGNNNN"[(sites[j].ori&0x7)])<<'\t'<<abbv[type1]<<'\t'<<q_cns<<'\t'
+ <<("ACTGNNNN"[base1])<<'\t'<<(sites[j].q_sum[base1]==0?0:sites[j].q_sum[base1]/sites[j].count_uni[base1])<<'\t'<<sites[j].count_uni[base1]<<'\t'<<sites[j].count_all[base1]<<'\t'
+ <<("ACTGNNNN"[base2])<<'\t'<<(sites[j].q_sum[base2]==0?0:sites[j].q_sum[base2]/sites[j].count_uni[base2])<<'\t'<<sites[j].count_uni[base2]<<'\t'<<sites[j].count_all[base2]<<'\t'
+ <<sites[j].depth<<'\t'<<showpoint<<rank_sum_test_value<<'\t'<<(sites[j].depth==0?255:(double)(sites[j].repeat_time)/sites[j].depth)<<'\t'<<((sites[j].ori&8)?1:0)<<endl;
+ }
+ else if(base1<4) {
+ consensus<<call_name<<'\t'<<(sites[j].pos+1)<<'\t'<<("ACTGNNNN"[(sites[j].ori&0x7)])<<'\t'<<abbv[type1]<<'\t'<<q_cns<<'\t'
+ <<("ACTGNNNN"[base1])<<'\t'<<(sites[j].q_sum[base1]==0?0:sites[j].q_sum[base1]/sites[j].count_uni[base1])<<'\t'<<sites[j].count_uni[base1]<<'\t'<<sites[j].count_all[base1]<<'\t'
+ <<"N\t0\t0\t0\t"
+ <<sites[j].depth<<'\t'<<showpoint<<rank_sum_test_value<<'\t'<<(sites[j].depth==0?255:(double)(sites[j].repeat_time)/sites[j].depth)<<'\t'<<((sites[j].ori&8)?1:0)<<endl;
+ }
+ else {
+ consensus<<call_name<<'\t'<<(sites[j].pos+1)<<"\tN\tN\t0\tN\t0\t0\t0\tN\t0\t0\t0\t0\t1.000\t255.000\t0"<<endl;
+ }
+ }
+ }
+ else {
+ if(base1<4 && base2<4) {
+ baseinfo<<call_name<<'\t'<<(sites[j].pos+1)<<'\t'<<("ACTGNNNN"[(sites[j].ori&0x7)])<<'\t'<<abbv[type1]<<'\t'<<q_cns<<'\t'
+ <<("ACTGNNNN"[base1])<<'\t'<<(sites[j].q_sum[base1]==0?0:sites[j].q_sum[base1]/sites[j].count_uni[base1])<<'\t'<<sites[j].count_uni[base1]<<'\t'<<sites[j].count_all[base1]<<'\t'
+ <<("ACTGNNNN"[base2])<<'\t'<<(sites[j].q_sum[base2]==0?0:sites[j].q_sum[base2]/sites[j].count_uni[base2])<<'\t'<<sites[j].count_uni[base2]<<'\t'<<sites[j].count_all[base2]<<'\t'
+ <<sites[j].depth<<'\t'<<showpoint<<rank_sum_test_value<<'\t'<<(sites[j].depth==0?255:(double)(sites[j].repeat_time)/sites[j].depth)<<'\t'<<((sites[j].ori&8)?1:0)<<endl;
+ }
+ else if(base1<4) {
+ baseinfo<<call_name<<'\t'<<(sites[j].pos+1)<<'\t'<<("ACTGNNNN"[(sites[j].ori&0x7)])<<'\t'<<abbv[type1]<<'\t'<<q_cns<<'\t'
+ <<("ACTGNNNN"[base1])<<'\t'<<(sites[j].q_sum[base1]==0?0:sites[j].q_sum[base1]/sites[j].count_uni[base1])<<'\t'<<sites[j].count_uni[base1]<<'\t'<<sites[j].count_all[base1]<<'\t'
+ <<"N\t0\t0\t0\t"
+ <<sites[j].depth<<'\t'<<showpoint<<rank_sum_test_value<<'\t'<<(sites[j].depth==0?255:(double)(sites[j].repeat_time)/sites[j].depth)<<'\t'<<((sites[j].ori&8)?1:0)<<endl;
+ }
+ else {
+ baseinfo<<call_name<<'\t'<<(sites[j].pos+1)<<"\tN\tN\t0\tN\t0\t0\t0\tN\t0\t0\t0\t0\t1.000\t255.000\t0"<<endl;
+ }
+ }
+ //if(sites[j].pos == 250949) {
+ // exit(1);
+ //}
+ }
+ delete [] real_p_prior;
+ delete [] pcr_dep_count;
+ delete [] likelihoods;
+ return 1;
+}
+
+int Call_win::soap2cns(std::ifstream & alignment, std::ofstream & consensus, std::ofstream & baseinfo, Genome * genome, Prob_matrix * mat, Parameter * para) {
+ Soap_format soap;
+ map<Chr_name, Chr_info*>::iterator current_chr, prev_chr;
+ current_chr = prev_chr = genome->chromosomes.end();
+ int coord, sub;
+ int last_start(0);
+ bool recycled(false);
+ for(std::string line; getline(alignment, line);) {
+ std::istringstream s(line);
+ if( s>> soap ) {
+ //cerr<<"A"<<soap.get_pos()<<endl;
+ //exit(1);
+ if(soap.get_pos() < 0) {
+ continue;
+ }
+ if (current_chr == genome->chromosomes.end() || current_chr->first != soap.get_chr_name()) {
+ if(current_chr != genome->chromosomes.end() ) {
+ recycled = false;
+ while(current_chr->second->length() > sites[win_size-1].pos) {
+ if (!para->region_only || current_chr->second->is_in_region_win(last_start)) {
+ //cerr<<"at"<<soap.get_pos()<<"Called"<<last_start<<endl;
+ if(last_start > sites[win_size-1].pos) {
+ initialize((last_start/win_size)*win_size);
+ }
+ call_cns(current_chr->first, current_chr->second, win_size, mat, para, consensus, baseinfo);
+ last_start = sites[win_size-1].pos;
+ recycled = false;
+ }
+ if (!para->region_only) {
+ //cerr<<"recycled"<<last_start<<endl;
+ recycle();
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else if (!recycled) {
+ //cerr<<"recycled"<<" "<<last_start<<endl;
+ if (last_start>(sites[win_size-1].pos)) {
+ cerr<<"Unexpected "<<last_start<<">"<<(sites[win_size-1].pos)<<endl;
+ exit(1);
+ if ((last_start+1)%win_size!=0) {
+ cerr<<"Assertion Error!"<<last_start<<">"<<sites[win_size-1].pos<<endl;
+ exit(1);
+ }
+ initialize(last_start-win_size+1);
+ }
+ else {
+ if (current_chr->second->is_in_region_win(sites[win_size].pos)) {
+ recycle();
+ }
+ else {
+ deep_init(sites[win_size].pos);
+ }
+ }
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else {
+ assert((last_start+1)%win_size==0);
+ last_start += win_size;
+ }
+ }
+ // The last window
+ if(last_start > sites[win_size-1].pos) {
+ initialize((last_start/win_size)*win_size);
+ }
+ call_cns(current_chr->first, current_chr->second, current_chr->second->length()%win_size, mat, para, consensus, baseinfo);
+ }
+ current_chr = genome->chromosomes.find(soap.get_chr_name());
+ initialize(0);
+ last_start = 0;
+ cerr<<"Processing "<<current_chr->first<<endl;
+ }
+ else {
+ ;
+ }
+ if (soap.get_pos()+soap.get_read_len()>=current_chr->second->length()) {
+ continue;
+ }
+ if (para->region_only && (current_chr->second->get_region() == NULL || !current_chr->second->is_in_region(soap.get_pos()))) {
+ continue;
+ }
+ if(soap.get_pos() < last_start) {
+ cerr<<"Errors in sorting:"<<soap.get_pos()<<"<"<<last_start<<endl;
+ exit(255);
+ }
+ recycled = false;
+ while (soap.get_pos()/win_size > last_start/win_size ) {
+ if (!para->region_only || current_chr->second->is_in_region_win(last_start)) {
+ //cerr<<"at"<<soap.get_pos()<<"Called"<<last_start<<endl;
+ if(last_start > sites[win_size-1].pos) {
+ initialize((last_start/win_size)*win_size);
+ }
+ call_cns(current_chr->first, current_chr->second, win_size, mat, para, consensus, baseinfo);
+ last_start = sites[win_size-1].pos;
+ recycled = false;
+ }
+ if (!para->region_only) {
+ //cerr<<"recycled"<<last_start<<endl;
+ recycle();
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else if (!recycled) {
+ //cerr<<"recycled"<<" "<<last_start<<endl;
+ if (last_start>(sites[win_size-1].pos)) {
+ cerr<<"Unexpected "<<last_start<<">"<<(sites[win_size-1].pos)<<endl;
+ exit(1);
+ if ((last_start+1)%win_size!=0) {
+ cerr<<"Assertion Error!"<<last_start<<">"<<sites[win_size-1].pos<<endl;
+ exit(1);
+ }
+ initialize(last_start-win_size+1);
+ }
+ else {
+ if (current_chr->second->is_in_region_win(sites[win_size].pos)) {
+ recycle();
+ }
+ else {
+ deep_init(sites[win_size].pos);
+ }
+ }
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else {
+ assert((last_start+1)%win_size==0);
+ last_start += win_size;
+ }
+ //if ((last_start+1)/win_size==1000) {
+ // cerr<<"Called "<<last_start;
+ //}
+ }
+ //cerr<<"die"<<endl;
+ //exit(1);
+ last_start=soap.get_pos();
+ for(coord=0; coord<soap.get_read_len(); coord++){
+ if( (soap.get_pos()+coord)/win_size == soap.get_pos()/win_size ) {
+ // In the same sliding window
+ sub = (soap.get_pos()+coord) % win_size;
+ }
+ else {
+ sub = (soap.get_pos()+coord) % win_size + win_size; // Use the tail to store the info so that it won't intervene the uncalled bases
+ }
+ sites[sub].depth += 1;
+ sites[sub].repeat_time += soap.get_hit();
+ if((soap.is_N(coord)) || soap.get_qual(coord)<para->q_min || sites[sub].dep_uni >= 0xFF) {
+ // An N, low quality or meaningless huge depth
+ continue;
+ }
+ if(soap.get_hit() == 1) {
+ //exit((fprintf(stderr, "Wo Cao!\n")));
+ sites[sub].dep_uni += 1;
+ // Update the covering info: 4x2x64x64 matrix, base x strand x q_score x read_pos, 2-1-6-6 bits for each
+ if(soap.is_fwd()) {
+ // Binary strand: 0 for plus and 1 for minus
+ sites[sub].base_info[(((ubit64_t)(soap.get_base(coord)&0x6)|0))<<14 | ((ubit64_t)(soap.get_qual(coord)-para->q_min))<<8 | coord ] += 1;
+ }
+ else {
+ sites[sub].base_info[(((ubit64_t)(soap.get_base(coord)&0x6)|1))<<14 | ((ubit64_t)(soap.get_qual(coord)-para->q_min))<<8 | (soap.get_read_len()-1-coord) ] += 1;
+
+ }
+ sites[sub].count_uni[(soap.get_base(coord)>>1)&3] += 1;
+ sites[sub].q_sum[(soap.get_base(coord)>>1)&3] += (soap.get_qual(coord)-para->q_min);
+ }
+ else {
+ ;// Repeats
+ }
+ sites[sub].count_all[(soap.get_base(coord)>>1)&3] += 1;
+ }
+ }
+ }
+
+//The unprocessed tail of chromosome
+ recycled = false;
+ while(current_chr->second->length() > sites[win_size-1].pos) {
+ if (!para->region_only || current_chr->second->is_in_region_win(last_start)) {
+ //cerr<<"at"<<soap.get_pos()<<"Called"<<last_start<<endl;
+ if(last_start > sites[win_size-1].pos) {
+ initialize((last_start/win_size)*win_size);
+ }
+ call_cns(current_chr->first, current_chr->second, win_size, mat, para, consensus, baseinfo);
+ last_start = sites[win_size-1].pos;
+ recycled = false;
+ }
+ if (!para->region_only) {
+ //cerr<<"recycled"<<last_start<<endl;
+ recycle();
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else if (!recycled) {
+ //cerr<<"recycled"<<" "<<last_start<<endl;
+ if (last_start>(sites[win_size-1].pos)) {
+ cerr<<"Unexpected "<<last_start<<">"<<(sites[win_size-1].pos)<<endl;
+ exit(1);
+ if ((last_start+1)%win_size!=0) {
+ cerr<<"Assertion Error!"<<last_start<<">"<<sites[win_size-1].pos<<endl;
+ exit(1);
+ }
+ initialize(last_start-win_size+1);
+ }
+ else {
+ if (current_chr->second->is_in_region_win(sites[win_size].pos)) {
+ recycle();
+ }
+ else {
+ deep_init(sites[win_size].pos);
+ }
+ }
+ recycled = true;
+ last_start = sites[win_size-1].pos;
+ }
+ else {
+ assert((last_start+1)%win_size==0);
+ last_start += win_size;
+ }
+ }
+// The last window
+ if(last_start > sites[win_size-1].pos) {
+ initialize((last_start/win_size)*win_size);
+ }
+ call_cns(current_chr->first, current_chr->second, current_chr->second->length()%win_size, mat, para, consensus, baseinfo);
+
+ alignment.close();
+ consensus.close();
+ baseinfo.close();
+ return 1;
+}
diff --git a/chromosome.cc b/chromosome.cc
new file mode 100644
index 0000000..056e6fd
--- /dev/null
+++ b/chromosome.cc
@@ -0,0 +1,220 @@
+#include "soap_snp.h"
+
+bool Genome::add_chr(Chr_name & name) {
+ Chr_info * new_chr = new Chr_info;
+ pair<map<Chr_name, Chr_info*>::iterator, bool> insert_pair;
+ insert_pair=chromosomes.insert(pair<Chr_name, Chr_info*>(name,new_chr));
+ return insert_pair.second;
+}
+
+Genome::~Genome(){
+ for( map<Chr_name, Chr_info*>::iterator iter=chromosomes.begin(); iter!= chromosomes.end(); iter++ ){
+ ;
+ }
+}
+Chr_info::Chr_info(const Chr_info & other) {
+ dbsnp = other.dbsnp;
+ len = other.len;
+ if (len%capacity==0) {
+ bin_seq = new ubit64_t [len/capacity];
+ memcpy(bin_seq, other.bin_seq, sizeof(ubit64_t)*len/capacity);
+ }
+ else {
+ bin_seq = new ubit64_t [1+len/capacity];
+ memcpy(bin_seq, other.bin_seq, sizeof(ubit64_t)*len/capacity);
+ }
+}
+
+int Chr_info::binarize(std::string & seq) {
+ len = seq.length();
+ //cerr<<len<<endl;
+ // 4bit for each base
+ // Allocate memory
+ if (len%capacity==0) {
+ bin_seq = new ubit64_t [len/capacity];
+ memset(bin_seq,0,sizeof(ubit64_t)*len/capacity);
+ }
+ else {
+ bin_seq = new ubit64_t [1+len/capacity];
+ memset(bin_seq,0,sizeof(ubit64_t)*(1+len/capacity));
+ }
+
+ // Add each base, 7 is 0b111
+ for(std::string::size_type i=0;i!=seq.length();i++) {
+ bin_seq[i/capacity] |= ((((ubit64_t)seq[i]>>1)&7)<<(i%capacity*4));
+ }
+ return 1;
+}
+
+int Chr_info::insert_snp(std::string::size_type pos, Snp_info & snp_form) {
+ Snp_info * new_snp = new Snp_info;
+ *new_snp = snp_form;
+ pair<map<ubit64_t, Snp_info*>::iterator, bool> insert_pair;
+ insert_pair = dbsnp.insert(pair<ubit64_t, Snp_info*>(pos,new_snp));
+ if(insert_pair.second) {
+ // Successful insertion
+ // Modify the binary sequence! Mark SNPs
+ bin_seq[pos/capacity] |= (1ULL<<(pos%capacity*4+3));
+ }
+ else {
+ cerr<<"Warning: Snp insertion failed\t"<<pos<<endl;
+ return 0;
+ }
+ return 1;
+}
+
+int Chr_info::set_region(int start, int end) {
+ if(start<0) {
+ start = 0;
+ }
+ else if (start >= len) {
+ start = len;
+ }
+
+ if(end<0) {
+ end = 0;
+ }
+ else if (end >= len) {
+ end = len;
+ }
+ if (start > end) {
+ cerr<<"Invalid region: "<<start<<"-"<<end<<endl;
+ exit(255);
+ }
+ // Specific mask
+ if(start/64 == end/64) {
+ region_mask[start/64] |= ((~((~(0ULL))<<(end-start+1)))<<(63-end%64));
+ }
+ else {
+ if(start % 64) {
+ region_mask[start/64] |= (~((~(0ULL))<<(64-start%64)));
+ }
+ else {
+ region_mask[start/64] = ~(0ULL);
+ }
+ region_mask[end/64] |= ((~(0ULL))<<(63-end%64));
+ if(end/64-start/64>1) {
+ memset(region_mask+start/64+1, 0xFF, sizeof(ubit64_t)*(end/64-start/64-1));
+ }
+ }
+ // Window mask
+ start /= global_win_size; end /= global_win_size;
+ //cerr<<start<<"\t"<<end<<endl;
+ if(start/64 == end/64) {
+ region_win_mask[start/64] |= ((~((~(0ULL))<<(end-start+1)))<<(63-end%64));
+ }
+ else {
+ if(start % 64) {
+ region_win_mask[start/64] |= (~((~(0ULL))<<(64-start%64)));
+ }
+ else {
+ region_win_mask[start/64] = ~(0ULL);
+ }
+ region_win_mask[end/64] |= ((~(0ULL))<<(63-end%64));
+ if(end/64-start/64>1) {
+ memset(region_win_mask+start/64+1, 0xFF, sizeof(ubit64_t)*(end/64-start/64-1));
+ }
+ }
+ return 1;
+}
+
+int Chr_info::region_mask_ini(){
+ //Specific mask
+ if(len%64==0) {
+ region_mask = new ubit64_t [len/64];
+ memset(region_mask, 0, sizeof(ubit64_t)*(len/64));
+ }
+ else {
+ region_mask = new ubit64_t [len/64+1];
+ memset(region_mask, 0, sizeof(ubit64_t)*(len/64+1));
+ }
+ //Window mask
+ int win_len = len/global_win_size +1;
+ if(win_len%64==0) {
+ region_win_mask = new ubit64_t [win_len/64];
+ memset(region_win_mask, 0, sizeof(ubit64_t)*(win_len/64));
+ }
+ else {
+ region_win_mask = new ubit64_t [win_len/64+1];
+ memset(region_win_mask, 0, sizeof(ubit64_t)*(win_len/64+1));
+ }
+ return 1;
+}
+
+int Genome::read_region(std::ifstream & region, Parameter * para) {
+ Chr_name current_name(""), prev_name("");
+ int start, end;
+ map<Chr_name, Chr_info*>::iterator chr_iter;
+ for(std::string buff;getline(region,buff);) {
+ std::istringstream s(buff);
+ if(s>>current_name>>start>>end) {
+ if(current_name != prev_name) {
+ chr_iter = chromosomes.find(current_name);
+ if(chr_iter == chromosomes.end()) {
+ cerr<<"Unexpected Chromosome:"<<current_name<<endl;
+ continue;
+ }
+ if(NULL == chr_iter->second->get_region()) {
+ chr_iter->second->region_mask_ini();
+ }
+ }
+ chr_iter->second->set_region(start-para->read_length, end-1);
+ prev_name = current_name;
+ }
+ else {
+ cerr<<"Wrong format in target region file"<<endl;
+ return 0;
+ }
+ }
+ return 1;
+}
+
+Genome::Genome(std::ifstream &fasta, std::ifstream & known_snp) {
+ std::string seq("");
+ Chr_name current_name("");
+ map<Chr_name, Chr_info*>::iterator chr_iter;
+ for(std::string buff;getline(fasta,buff);) {
+ if('>' == buff[0]) {
+ // Fasta id
+ // Deal with previous chromosome
+ if( chromosomes.find(current_name) != chromosomes.end()) {
+ chr_iter = chromosomes.find(current_name);
+ chr_iter->second->binarize(seq);
+ }
+ // Insert new chromosome
+ std::string::size_type i;
+ for(i=1;!isspace(buff[i]) && i != buff.length();i++) {
+ ;
+ }
+ Chr_name new_chr_name(buff,1,i-1);
+ if(! add_chr(new_chr_name)) {
+ std::cerr<<"Insert Chromosome "<<new_chr_name<<" Failed!\n";
+ }
+ current_name = new_chr_name;
+ seq = "";
+ }
+ else {
+ seq += buff;
+ }
+ }
+ if(seq.length() != 0 && chromosomes.find(current_name) != chromosomes.end()) {
+ chr_iter = chromosomes.find(current_name);
+ chr_iter->second->binarize(seq);
+ }
+ if( known_snp ) {
+ Chr_name current_name;
+ Snp_info snp_form;
+ std::string::size_type pos;
+ for(std::string buff;getline(known_snp, buff);) {
+ // Format: Chr\tPos\thapmap?\tvalidated?\tis_indel?\tA\tC\tT\tG\trsID\n
+ std::istringstream s(buff);
+ s>>current_name>>pos;
+ s>>snp_form;
+ if( chromosomes.find(current_name) != chromosomes.end()) {
+ // The SNP is located on an valid chromosme
+ pos -= 1; // Coordinates starts from 0
+ (chromosomes.find(current_name)->second)->insert_snp(pos, snp_form);
+ }
+ }
+ }
+}
diff --git a/debian/README.Debian b/debian/README.Debian
deleted file mode 100644
index 754e8ef..0000000
--- a/debian/README.Debian
+++ /dev/null
@@ -1,10 +0,0 @@
-soapsnp for Debian
-------------------
-
-** PACKAGING IS NOT YET COMPLETED **
-
-Ideas for improvements of this package:
- * platform-specific optimisations
- * we should have some public use cases together with getData
-
- -- Steffen Moeller <moeller at debian.org> Sun, 22 Apr 2012 01:26:41 +0200
diff --git a/debian/changelog b/debian/changelog
deleted file mode 100644
index 7ed88b8..0000000
--- a/debian/changelog
+++ /dev/null
@@ -1,9 +0,0 @@
-soapsnp (1.03-1) UNRELEASED; urgency=low
-
- [ Steffen Moeller ]
- * Initial release (Closes: #nnnn)
-
- [ Andreas Tille ]
- * cme
-
- -- Steffen Moeller <moeller at debian.org> Sun, 22 Apr 2012 01:26:41 +0200
diff --git a/debian/compat b/debian/compat
deleted file mode 100644
index f599e28..0000000
--- a/debian/compat
+++ /dev/null
@@ -1 +0,0 @@
-10
diff --git a/debian/control b/debian/control
deleted file mode 100644
index 617bccc..0000000
--- a/debian/control
+++ /dev/null
@@ -1,37 +0,0 @@
-Source: soapsnp
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller at debian.org>
-Section: science
-Priority: optional
-Build-Depends: debhelper (>= 10),
- libboost-iostreams-dev
-Standards-Version: 4.1.2
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/soap/soapsnp/trunk
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/soap/soapsnp/trunk
-Homepage: http://soap.genomics.org.cn/soapsnp.html
-
-Package: soapsnp
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends}
-Suggests: genomics.cn-soapsnp
-Description: <insert up to 60 chars description>
- For getting ideas on the cause of diseases or their response to
- therapy, and for understanding either for a particular patient,
- doctors around the globe are starting to look at the genes or the
- whole genome and how that sequence is different from a healthy /
- well responding individual.
- .
- SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis
- Package). The program is a resequencing utility. It assembles the
- consensus sequence for the genome of a newly sequenced individual based
- on the alignment of the raw sequencing reads on a known reference. SNPs
- can then be identified on the consensus sequence through the comparison
- with the reference.
- .
- SOAPsnp uses a method based on Bayes' theorem (the reverse probability
- model) to call consensus genotype by carefully considering the data
- quality, alignment, and recurring experimental errors. All these kinds
- of information was integrated into a single quality score for each base
- in PHRED scale to measure the accuracy of consensus calling. Currently,
- it supports the alignment format of SOAPaligner (soap2).
diff --git a/debian/copyright b/debian/copyright
deleted file mode 100644
index b2d0b99..0000000
--- a/debian/copyright
+++ /dev/null
@@ -1,28 +0,0 @@
-Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: soapsnp
-Source: <url://example.com>
-
-Files: *
-Copyright: 2008 BGI shenzhen <soap at genomics.org.cn>
-License: GPL-3.0+
-
-Files: debian/*
-Copyright: 2012 Steffen Moeller <moeller at debian.org>
-License: GPL-3.0+
-
-License: GPL-3.0+
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>.
- .
- On Debian systems, the complete text of the GNU General
- Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/docs b/debian/docs
deleted file mode 100644
index 8178c76..0000000
--- a/debian/docs
+++ /dev/null
@@ -1 +0,0 @@
-readme
diff --git a/debian/patches/Makefile.patch b/debian/patches/Makefile.patch
deleted file mode 100644
index d89a5d0..0000000
--- a/debian/patches/Makefile.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-Index: soapsnp-1.03/makefile
-===================================================================
---- soapsnp-1.03.orig/makefile 2009-05-25 09:49:19.000000000 +0200
-+++ soapsnp-1.03/makefile 2012-04-22 01:27:43.714978426 +0200
-@@ -1,6 +1,6 @@
- DEFINE =
- CXX = g++
--CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
-+CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops #-mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
-
- LFLAGS = -lz
-
diff --git a/debian/patches/series b/debian/patches/series
deleted file mode 100644
index 5b1c0a4..0000000
--- a/debian/patches/series
+++ /dev/null
@@ -1 +0,0 @@
-Makefile.patch
diff --git a/debian/rules b/debian/rules
deleted file mode 100755
index e57588d..0000000
--- a/debian/rules
+++ /dev/null
@@ -1,11 +0,0 @@
-#!/usr/bin/make -f
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-%:
- dh $@
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
diff --git a/debian/source/format b/debian/source/format
deleted file mode 100644
index 163aaf8..0000000
--- a/debian/source/format
+++ /dev/null
@@ -1 +0,0 @@
-3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
deleted file mode 100644
index 6651c34..0000000
--- a/debian/upstream/metadata
+++ /dev/null
@@ -1,14 +0,0 @@
-Contact: soap at genomics.org.cn
-Homepage: http://soap.genomics.org.cn/soapsnp.html
-Reference:
- DOI: 10.1101/gr.088013.108
- Eprint: http://genome.cshlp.org/content/19/6/1124.full.pdf+html
- Journal: Genome Res.
- PMID: 19420381
- Author: Li R and Li Y and Fang X and Yang H and Wang J and Kristiansen K and Wang J.
- Title: SNP detection for massively parallel whole-genome resequencing
- URL: http://genome.cshlp.org/content/19/6/1124.long
- Year: 2009
- Volume: 19
- Number: 6
- Pages: 1124-1132
diff --git a/debian/watch b/debian/watch
deleted file mode 100644
index 5a50eee..0000000
--- a/debian/watch
+++ /dev/null
@@ -1,2 +0,0 @@
-version=3
-http://soap.genomics.org.cn/soapsnp.html down/SOAPsnp-v(.*)\.tar\.gz
diff --git a/main.cc b/main.cc
new file mode 100644
index 0000000..055537c
--- /dev/null
+++ b/main.cc
@@ -0,0 +1,332 @@
+#include "soap_snp.h"
+#include <getopt.h>
+
+using namespace std;
+
+int usage() {
+ cerr<<"SoapSNP"<<endl;
+ cerr<<"Compulsory Parameters:"<<endl;
+ cerr<<"-i <FILE> Input SORTED Soap Result"<<endl;
+ cerr<<"-d <FILE> Reference Sequence in fasta format"<<endl;
+ cerr<<"-o <FILE> Output consensus file"<<endl;
+ cerr<<"Optional Parameters:(Default in [])"<<endl;
+ cerr<<"-z <Char> ASCII chracter standing for quality==0 [@]"<<endl;
+ cerr<<"-g <Double> Global Error Dependency Coefficient, 0.0(complete dependent)~1.0(complete independent)[0.9]"<<endl;
+ cerr<<"-p <Double> PCR Error Dependency Coefficient, 0.0(complete dependent)~1.0(complete independent)[0.5]"<<endl;
+ cerr<<"-r <Double> novel altHOM prior probability [0.0005]"<<endl;
+ cerr<<"-e <Double> novel HET prior probability [0.0010]"<<endl;
+ cerr<<"-t set transition/transversion ratio to 2:1 in prior probability"<<endl;
+ cerr<<"-s <FILE> Pre-formated dbSNP information"<<endl;
+ cerr<<"-2 specify this option will REFINE SNPs using dbSNPs information [Off]"<<endl;
+ cerr<<"-a <Double> Validated HET prior, if no allele frequency known [0.1]"<<endl;
+ cerr<<"-b <Double> Validated altHOM prior, if no allele frequency known[0.05]"<<endl;
+ cerr<<"-j <Double> Unvalidated HET prior, if no allele frequency known [0.02]"<<endl;
+ cerr<<"-k <Double> Unvalidated altHOM rate, if no allele frequency known[0.01]"<<endl;
+ cerr<<"-u Enable rank sum test to give HET further penalty for better accuracy. [Off]"<<endl;
+ //cerr<<"-n Enable binomial probability calculation to give HET for better accuracy. [Off]"<<endl;
+ cerr<<"-m Enable monoploid calling mode, this will ensure all consensus as HOM and you probably should SPECIFY higher altHOM rate. [Off]"<<endl;
+ cerr<<"-q Only output potential SNPs. Useful in Text output mode. [Off]"<<endl;
+ cerr<<"-M <FILE> Output the quality calibration matrix; the matrix can be reused with -I if you rerun the program"<<endl;
+ cerr<<"-I <FILE> Input previous quality calibration matrix. It cannot be used simutaneously with -M"<<endl;
+ cerr<<"-L <short> maximum length of read [45]"<<endl;
+ cerr<<"-Q <short> maximum FASTQ quality score [40]"<<endl;
+ cerr<<"-F <int> Output format. 0: Text; 1: GLFv2; 2: GPFv2.[0]"<<endl;
+ cerr<<"-E <String> Extra headers EXCEPT CHROMOSOME FIELD specified in GLFv2 output. Format is \"TypeName1:DataName1:TypeName2:DataName2\"[""]"<<endl;
+ cerr<<"-T <FILE> Only call consensus on regions specified in FILE. Format: ChrName\\tStart\\tEnd."<<endl;
+ //cerr<<"-S <FILE> Output summary of consensus"<<endl;
+ cerr<<"-h Display this help"<<endl;
+ exit(1);
+ return 0;
+}
+
+int readme() {
+ return usage();
+}
+
+int main ( int argc, char * argv[]) {
+ // This part is the default values of all parameters
+ Parameter * para = new Parameter;
+ std::string alignment_name, consensus_name("");
+ bool is_matrix_in = false; // Generate the matrix or just read it?
+ int c;
+ Files files;
+ while((c=getopt(argc,argv,"i:d:o:z:g:p:r:e:ts:2a:b:j:k:unmqM:I:L:Q:S:F:E:T:h")) != -1) {
+ switch(c) {
+ case 'i':
+ {
+ // Soap Alignment Result
+ files.soap_result.clear();
+ files.soap_result.open(optarg);
+ if( ! files.soap_result) {
+ cerr<<"No such file or directory:"<<optarg<<endl;
+ exit(1);
+ }
+ alignment_name = optarg;
+ break;
+ }
+ case 'd':
+ {
+ // The reference genome in fasta format
+ files.ref_seq.clear();
+ files.ref_seq.open(optarg);
+ if( ! files.ref_seq) {
+ cerr<<"No such file or directory:"<<optarg<<endl;
+ exit(1);
+ }
+ files.ref_seq.clear();
+ break;
+ }
+ case 'o':
+ {
+ consensus_name = optarg;
+ break;
+ }
+ case 'z':
+ {
+ // The char stands for quality==0 in fastq format
+ para->q_min = optarg[0];
+ if(para->q_min == 33) {
+ clog<<"Standard Fastq System Set"<<endl;
+ }
+ else if(para->q_min == 64) {
+ clog<<"Illumina Fastq System Set"<<endl;
+ }
+ else {
+ clog<<"Other types of Fastq files?? Are you sure?"<<endl;
+ }
+ para->q_max = para->q_min + 40;
+ break;
+ }
+ case 'g':
+ {
+ para->global_dependency= log10(atof(optarg));
+ break;
+ }
+ case 'p':
+ {
+ para->pcr_dependency= log10(atof(optarg));
+ break;
+ }
+ case 'r':
+ {
+ para->althom_novel_r = atof(optarg);
+ break;
+ }
+ case 'e':
+ {
+ para->het_novel_r=atof(optarg);
+ break;
+ }
+ case 't':
+ {
+ para->transition_dominant=true;
+ break;
+ }
+ case 's':
+ {
+ // Optional: A pre-formated dbSNP table
+ files.dbsnp.clear();
+ files.dbsnp.open(optarg);
+ if( ! files.ref_seq) {
+ cerr<<"No such file or directory:"<<optarg<<endl;
+ exit(1);
+ }
+ files.dbsnp.clear();
+ break;
+ }
+ case '2':
+ {
+ // Refine prior probability based on dbSNP information
+ para->refine_mode = true;
+ break;
+ }
+ case 'a':
+ {
+ para->althom_val_r=atof(optarg);
+ break;
+ }
+ case 'b':
+ {
+ para->het_val_r=atof(optarg);
+ break;
+ }
+ case 'j':
+ {
+ para->althom_unval_r=atof(optarg);
+ break;
+ }
+ case 'k':
+ {
+ para->het_unval_r=atof(optarg);
+ break;
+ }
+ case 'u':
+ {
+ para->rank_sum_mode = true;
+ break;
+ }
+ case 'n':
+ {
+ para->binom_mode = true;
+ break;
+ }
+ case 'm':
+ {
+ para->is_monoploid=1;
+ break;
+ }
+ case 'q':
+ {
+ para->is_snp_only=1;
+ break;
+ }
+ case 'M':
+ {
+ files.matrix_file.close(); files.matrix_file.clear();
+ // Output the calibration matrix
+ files.matrix_file.open(optarg, fstream::out);
+ if( ! files.matrix_file) {
+ cerr<<"Cannot creat file :"<<optarg<<endl;
+ exit(1);
+ }
+ files.matrix_file.clear();
+ break;
+ }
+ case 'I':
+ {
+ files.matrix_file.close(); files.matrix_file.clear();
+ // Input the calibration matrix
+ files.matrix_file.open(optarg, fstream::in);
+ if( ! files.matrix_file) {
+ cerr<<"No such file or directory:"<<optarg<<endl;
+ exit(1);
+ }
+ files.matrix_file.clear();
+ is_matrix_in = true;
+ break;
+ }
+ case 'S':
+ {
+ //files.summary.open(optarg);
+ //// Output the summary of consensus
+ //if( ! files.summary ) {
+ // cerr<<"No such file or directory: "<<optarg<<endl;
+ // exit(1);
+ //}
+ break;
+ }
+ case 'L':
+ {
+ para->read_length = atoi(optarg);
+ break;
+ }
+ case 'Q':
+ {
+ para->q_max = optarg[0];
+ if(para->q_max < para->q_min) {
+ cerr<< "FASTQ quality character error: Q_MAX > Q_MIN" <<endl;
+ }
+ break;
+ }
+ case 'F': {
+ para->glf_format = atoi(optarg);
+ break;
+ }
+ case 'E': {
+ para->glf_header = optarg;
+ break;
+ }
+ case 'T': {
+ files.region.clear();
+ files.region.open(optarg);
+ files.region.clear();
+ para->region_only = true;
+ break;
+ }
+ case 'h':readme();break;
+ case '?':usage();break;
+ default: cerr<<"Unknown error in command line parameters"<<endl;
+ }
+ }
+ if( consensus_name=="" || !files.ref_seq || !files.soap_result ) {
+ // These are compulsory parameters
+ usage();
+ }
+ if ( ! para->glf_format ) {
+ // Normal SOAPsnp tab-delimited text format
+ files.consensus.clear();
+ files.consensus.open(consensus_name.c_str());
+ if( ! files.consensus ) {
+ cerr<<"Cannot creat file:" <<consensus_name<<endl;
+ exit(1);
+ }
+ files.consensus.clear();
+ }
+ else {
+ // SOAPsnp-defined GLF and baseinfo format
+ files.consensus.clear();
+ files.consensus.open(consensus_name.c_str(), ios::binary);
+ if(!files.consensus) {
+ cerr<<"Cannot creat file:" <<consensus_name<<endl;
+ exit(1);
+ }
+ files.consensus.clear();
+
+ files.baseinfo.clear();
+ string baseinfo_name = consensus_name + ".baseinfo";
+ files.baseinfo.open(baseinfo_name.c_str());
+ if(!files.baseinfo) {
+ cerr<<"Cannot creat file:" <<baseinfo_name<<endl;
+ exit(1);
+ }
+ files.baseinfo.clear();
+
+ files.o_region.clear();
+ string o_region_name = consensus_name + ".index";
+ files.o_region.open(o_region_name.c_str());
+ if(!files.o_region) {
+ cerr<<"Cannot creat file:" <<o_region_name<<endl;
+ exit(1);
+ }
+ files.o_region.clear();
+ }
+
+ //Read the chromosomes into memory
+ Genome * genome = new Genome(files.ref_seq, files.dbsnp);
+ files.ref_seq.close();
+ files.dbsnp.close();
+ clog<<"Reading Chromosome and dbSNP information Done."<<endl;
+ if(para->region_only && files.region) {
+ genome->read_region(files.region, para);
+ clog<<"Read target region done."<<endl;
+ }
+
+ Prob_matrix * mat = new Prob_matrix;
+ if( ! is_matrix_in) {
+ //Read the soap result and give the calibration matrix
+ mat->matrix_gen(files.soap_result, para, genome);
+ if (files.matrix_file) {
+ mat->matrix_write(files.matrix_file, para);
+ }
+ }
+ else {
+ mat->matrix_read(files.matrix_file, para);
+ }
+ files.matrix_file.close();
+ clog<<"Correction Matrix Done!"<<endl;
+ mat->prior_gen(para);
+ mat->rank_table_gen();
+ Call_win info(para->read_length);
+ info.initialize(0);
+ //Call the consensus
+ files.soap_result.close();
+ files.soap_result.clear();
+ files.soap_result.open(alignment_name.c_str());
+ files.soap_result.clear();
+ info.soap2cns(files.soap_result, files.consensus, files.baseinfo, genome, mat, para);
+ files.soap_result.close();
+ files.consensus.close();
+ cerr<<"Consensus Done!"<<endl;
+ return 0;
+}
+
diff --git a/makefile b/makefile
new file mode 100644
index 0000000..b92bc7c
--- /dev/null
+++ b/makefile
@@ -0,0 +1,18 @@
+DEFINE =
+CXX = g++
+CXXFLAGS = -fomit-frame-pointer -O3 -ffast-math -funroll-loops -mmmx -msse -msse2 -msse3 -fmessage-length=0 #-MMD -MP -MF #-g3 -Wall -maccumulate-outgoing-args
+
+LFLAGS = -lz
+
+all: soapsnp
+.PHONY: all
+
+objects: call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o
+$(objects): %.o: soap_snp.h makefile
+
+soapsnp: call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o makefile
+ $(CXX) $(CXXFLAGS) call_genotype.o chromosome.o matrix.o normal_dis.o prior.o rank_sum.o main.o -o soapsnp $(LFLAGS)
+
+.PHONY: clean
+clean:
+ rm -f *.o soapsnp
diff --git a/matrix.cc b/matrix.cc
new file mode 100644
index 0000000..f6cbcc5
--- /dev/null
+++ b/matrix.cc
@@ -0,0 +1,219 @@
+#include "soap_snp.h"
+Prob_matrix::Prob_matrix(){
+ int i;
+ p_matrix = new rate_t [256*256*4*4]; // 8bit: q_max, 8bit: read_len, 4bit: number of types of all mismatch/match 4x4
+ p_prior = new rate_t [8*4*4]; // 8(ref ACTGNNNN) * diploid(4x4)
+ base_freq = new rate_t [4]; // 4 base
+ type_likely = new rate_t [16+1]; //The 17th element rate_t[16] will be used in comparison
+ type_prob = new rate_t [16+1];
+ p_rank = new rate_t [64*64*2048]; // 6bit: N; 5bit: n1; 11bit; T1
+ p_binom = new rate_t [256*256]; // Total * case
+ for(i=0;i!=256*256*4*4;i++) {
+ p_matrix[i] = 1.0;
+ }
+ for(i=0;i!=8*4*4;i++) {
+ p_prior[i] = 1.0;
+ }
+ for(i=0;i!=4;i++) {
+ base_freq[i] = 1.0;
+ }
+ for(i=0;i!=16+1;i++) {
+ type_likely[i] = 0.0; // LOG10 Scale
+ type_prob[i] = 0.0; // LOG10 Scale
+ }
+ for(i=0;i!=64*64*2048;i++) {
+ p_rank[i] = 1.0;
+ }
+ for(i=0;i!=256*256;i++) {
+ p_binom[i] = 1.0;
+ }
+}
+
+Prob_matrix::~Prob_matrix(){
+ delete [] p_matrix; // 8bit: q_max, 8bit: read_len, 4bit: number of types of all mismatch/match 4x4
+ delete [] p_prior; // 8(ref ACTGNNNN) * diploid(4x4)
+ delete [] base_freq; // 4 base
+ delete [] type_likely; //The 17th element rate_t[16] will be used in comparison
+ delete [] type_prob;
+ delete [] p_rank; // 6bit: N; 5bit: n1; 11bit; T1
+ delete [] p_binom; // Total * case;
+}
+
+int Prob_matrix::matrix_gen(std::ifstream & alignment, Parameter * para, Genome * genome) {
+ // Read Alignment files
+ Soap_format soap;
+ ubit64_t * count_matrix = new ubit64_t [256*256*4*4];
+ map<Chr_name, Chr_info*>::iterator current_chr;
+ current_chr = genome->chromosomes.end();
+ ubit64_t ref(0);
+ std::string::size_type coord;
+ for(std::string line; getline(alignment, line);) {
+ std::istringstream s(line);
+ if( s>> soap ) {
+ if(soap.get_pos() < 0) {
+ continue;
+ }
+ //cerr<<soap<<endl;
+ // In the overloaded "+" above, soap.position will be substracted by 1 so that coordiates start from 0
+ if (current_chr == genome->chromosomes.end() || current_chr->first != soap.get_chr_name()) {
+ current_chr = genome->chromosomes.find(soap.get_chr_name());
+ if(current_chr == genome->chromosomes.end()) {
+ for(map<Chr_name, Chr_info*>::iterator test = genome->chromosomes.begin();test != genome->chromosomes.end();test++) {
+ cerr<<'!'<<(test->first)<<'!'<<endl;
+ }
+ cerr<<"Assertion Failed: Chromosome: !"<<soap.get_chr_name()<<"! NOT found"<<endl;
+ exit(255);
+ }
+ }
+ else {
+ ;
+ }
+ if (soap.get_pos()+soap.get_read_len()>=current_chr->second->length()) {
+ continue;
+ }
+ if (soap.is_unique()) {
+ for(coord = 0; coord != soap.get_read_len(); coord++) {
+ if (soap.is_N(coord)) {
+ ;
+ }
+ else {
+ if(! (soap.get_pos()+coord<current_chr->second->length())) {
+ cerr<<soap<<endl;
+ cerr<<"The program found the above read has exceed the reference length:\n";
+ cerr<<"The read is aligned to postion: "<<soap.get_pos()<<" with read length: "<<soap.get_read_len()<<endl;
+ cerr<<"Reference: "<<current_chr->first<<" FASTA Length: "<<current_chr->second->length()<<endl;
+ exit(255);
+ }
+ ref = current_chr->second->get_bin_base(soap.get_pos()+coord);
+ if ( (ref&12) !=0 ) {
+ // This is an N on reference or a dbSNP which should be excluded from calibration
+ ;
+ }
+ else {
+ if(soap.is_fwd()) {
+ // forward strand
+ count_matrix[(((ubit64_t)soap.get_qual(coord))<<12) | (coord<<4) | ((ref&0x3)<<2) | (soap.get_base(coord)>>1)&3] += 1;
+ }
+ else {
+ // reverse strand
+ count_matrix[(((ubit64_t)soap.get_qual(coord))<<12) | ((soap.get_read_len()-1-coord)<<4) | ((ref&0x3)<<2) | (soap.get_base(coord)>>1)&3] += 1;
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+ ubit64_t o_base/*o_based base*/, t_base/*theorecical(supposed) base*/, type, sum[4], same_qual_count_by_type[16], same_qual_count_by_t_base[4], same_qual_count_total, same_qual_count_mismatch;
+ char q_char/*fastq quality char*/;
+
+ const ubit64_t sta_pow=10; // minimum number to say statistically powerful
+ for(q_char=para->q_min; q_char<=para->q_max ;q_char++) {
+ memset(same_qual_count_by_type, 0, sizeof(ubit64_t)*16);
+ memset(same_qual_count_by_t_base, 0, sizeof(ubit64_t)*4);
+ same_qual_count_total = 0;
+ same_qual_count_mismatch = 0;
+ for(coord=0; coord != para->read_length ; coord++) {
+ for(type=0;type!=16;type++) {
+ // If the sample is small, then we will not consider the effect of read cycle.
+ same_qual_count_by_type[type] += count_matrix[ ((ubit64_t)q_char<<12) | coord <<4 | type];
+ same_qual_count_by_t_base[(type>>2)&3] += count_matrix[ ((ubit64_t)q_char<<12) | coord <<4 | type];
+ same_qual_count_total += count_matrix[ ((ubit64_t)q_char<<12) | coord <<4 | type];
+ //cerr<<(int)type<<'\t'<<same_qual_count_by_type[type]<<'\t'<<same_qual_count_by_t_base[0]<<endl;
+ if(type % 5 != 0) {
+ // Mismatches
+ same_qual_count_mismatch += count_matrix[ ((ubit64_t)q_char<<12) | coord <<4 | type];
+ }
+ }
+ }
+ for(coord=0; coord != para->read_length ; coord++) {
+ //cerr<<(q_char)<<'\t'<<coord;
+ memset(sum, (ubit64_t)0, sizeof(ubit64_t)*4);
+ // Count of all ref base at certain coord and quality
+ for(type=0;type!=16;type++) {
+ sum[(type>>2)&3] += count_matrix[ ((ubit64_t)q_char<<12) | (coord <<4) | type]; // (type>>2)&3: the ref base
+ //cerr<<sum[type&3]<<endl;
+ }
+ for(t_base=0; t_base!=4; t_base++) {
+ for(o_base=0; o_base!=4; o_base++) {
+ //cerr<<'\t'<<count_matrix[ ((ubit64_t)q_char<<12) | (coord <<4) | (t_base<<2) | o_base];
+ if (count_matrix[ ((ubit64_t)q_char<<12) | (coord <<4) | (t_base<<2) | o_base] > sta_pow) {
+ // Statistically powerful
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = ((double)count_matrix[ ((ubit64_t)q_char<<12) | (coord <<4) | (t_base<<2) | o_base]) / sum[t_base];
+ }
+ else if (same_qual_count_by_type[t_base<<2|o_base] > sta_pow) {
+ // Smaller sample, given up effect from read cycle
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = ((double)same_qual_count_by_type[t_base<<2|o_base]) / same_qual_count_by_t_base[t_base];
+ }
+ else if (same_qual_count_total > 0){
+ // Too small sample, given up effect of mismatch types
+ if (o_base == t_base) {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = ((double)(same_qual_count_total-same_qual_count_mismatch))/same_qual_count_total;
+ }
+ else {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = ((double)same_qual_count_mismatch)/same_qual_count_total;
+ }
+ }
+ else {
+ ;
+ }
+
+ // For these cases like:
+ // Ref: G o_base: G x10 Ax5. When calculate the probability of this allele to be A,
+ // If there's no A in reference gives observation of G, then the probability will be zero,
+ // And therefore exclude the possibility of this pos to have an A
+ // These cases should be avoid when the dataset is large enough
+ // If no base with certain quality is o_based, it also doesn't matter
+ if( (p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base]==0) || p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] ==1) {
+ if (o_base == t_base) {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = (1-pow(10, -((q_char-para->q_min)/10.0)));
+ if(p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base]<0.25) {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = 0.25;
+ }
+ }
+ else {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = (pow(10, -((q_char-para->q_min)/10.0))/3);
+ if(p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base]>0.25) {
+ p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | (t_base<<2) | o_base] = 0.25;
+ }
+ }
+ }
+ }
+ }
+ }
+ //cerr<<'\t'<<same_qual_count_by_type[0]<<'\t'<<same_qual_count_by_t_base[0]<<endl;
+ }
+ delete [] count_matrix;
+
+ //memset(&p_matrix[((ubit64_t)para->q_max-para->q_min+1)<<12], 0, 256*256*4*4 - (para->q_max-para->q_min+1)*256*4*4);
+ // Note: from now on, the first 8 bit of p_matrix is its quality score, not the FASTQ char
+ return 1;
+}
+
+int Prob_matrix::matrix_read(std::fstream &mat_in, Parameter * para) {
+ int q_char, type;
+ std::string::size_type coord;
+ for(std::string line; getline(mat_in, line);) {
+ std::istringstream s(line);
+ s>>q_char>>coord;
+ for(type=0;type!=16;type++) {
+ s>>p_matrix [ ((ubit64_t)q_char<<12) | (coord <<4) | type];
+ //cerr<<q_char<<"|"<<coord<<"|"<<p_matrix [ ((ubit64_t)q_char<<12) | (coord <<4) | type]<<endl;
+ //exit(0);
+ }
+ }
+ return 1;
+}
+
+int Prob_matrix::matrix_write(std::fstream &mat_out, Parameter * para) {
+ for( char q_char = para->q_min; q_char <= para->q_max; q_char++ ) {
+ for( std::string::size_type coord=0; coord != para->read_length; coord++) {
+ mat_out<<((ubit64_t)q_char-para->q_min)<<'\t'<<coord;
+ for(char type=0;type!=16;type++) {
+ mat_out<<'\t'<<scientific<<showpoint<<setprecision(16)<<p_matrix [ ((ubit64_t)(q_char-para->q_min)<<12) | (coord <<4) | type];
+ }
+ mat_out<<endl;
+ }
+ }
+ return 1;
+}
diff --git a/normal_dis.cc b/normal_dis.cc
new file mode 100644
index 0000000..2ac0d8d
--- /dev/null
+++ b/normal_dis.cc
@@ -0,0 +1,24 @@
+#include "soap_snp.h"
+
+double Call_win::normal_value(double z) {
+ if (z>6.0 || z<-6.0) {
+ return 0.0;
+ }
+ else {
+ double b1 = 0.31938153;
+ double b2 = -0.356563782;
+ double b3 = 1.781477937;
+ double b4 = -1.821255978;
+ double b5 = 1.330274429;
+ double p = 0.2316419;
+ double c2 = 0.39894228;
+
+ double a = fabs(z);
+ double t = 1.0/(1.0+a*p);
+ double b = c2*exp((-z)*(z/2.0));
+ double n = ((((b5*t+b4)*t+b3)*t+b2)*t+b1)*t;
+ n = 1.0 - b*n;
+ if (z < 0.0) n = 1.0 - n;
+ return n>0.5?1-n:n;
+ }
+}
diff --git a/prior.cc b/prior.cc
new file mode 100644
index 0000000..344900f
--- /dev/null
+++ b/prior.cc
@@ -0,0 +1,97 @@
+#include "soap_snp.h"
+
+int Prob_matrix::prior_gen(Parameter * para) {
+ char t_base, allele1, allele2;
+ // Note, the above parameter should be changed to a more reasonable one
+ for(t_base=0;t_base!=4;t_base++) {
+ for(allele1=0;allele1!=4;allele1++) {
+ for(allele2=allele1;allele2!=4;allele2++) {
+ if(allele1 == t_base && allele2 == t_base) {
+ // refHOM
+ p_prior[t_base<<4|allele1<<2|allele2] = 1;
+ }
+ else if (allele1 == t_base || allele2 == t_base) {
+ // refHET: 1 ref 1 alt
+ p_prior[t_base<<4|allele1<<2|allele2] = para->het_novel_r;
+ }
+ else if (allele1 == allele2) {
+ // altHOM
+ p_prior[t_base<<4|allele1<<2|allele2] = para->althom_novel_r;
+ }
+ else {
+ // altHET: 2 diff alt base
+ p_prior[t_base<<4|allele1<<2|allele2] = para->het_novel_r * para->althom_novel_r;
+ }
+ if( para->transition_dominant && ((allele1^t_base) == 0x3 || (allele2^t_base) == 0x3)) {
+ // transition
+ p_prior[t_base<<4|allele1<<2|allele2] *= 4;
+ }
+ //std::cerr<<"ACTG"[t_base]<<"\t"<<"ACTG"[allele1]<<"ACTG"[allele2]<<"\t"<<p_prior[t_base<<4|allele1<<2|allele2]<<endl;
+ }
+ }
+ }
+ for(allele1=0;allele1!=4;allele1++) {
+ for(allele2=allele1;allele2!=4;allele2++) {
+ // Deal with N
+ p_prior[0x4<<4|allele1<<2|allele2] = (allele1==allele2? 1: (2*para->het_novel_r)) * 0.25 *0.25;
+ p_prior[0x5<<4|allele1<<2|allele2] = (allele1==allele2? 1: (2*para->het_novel_r)) * 0.25 *0.25;
+ p_prior[0x6<<4|allele1<<2|allele2] = (allele1==allele2? 1: (2*para->het_novel_r)) * 0.25 *0.25;
+ p_prior[0x7<<4|allele1<<2|allele2] = (allele1==allele2? 1: (2*para->het_novel_r)) * 0.25 *0.25;
+ }
+ }
+ return 1;
+}
+
+int Call_win::snp_p_prior_gen(double * real_p_prior, Snp_info* snp, Parameter * para, char ref) {
+ if (snp->is_indel()) {
+ return 0;
+ }
+ char base, allele1, allele2;
+ int allele_count;
+ allele_count = 0;
+ for (base=0; base != 4; base ++) {
+ if(snp->get_freq(base)>0) {
+ // The base is found in dbSNP
+ allele_count += 1;
+ }
+ }
+ if(allele_count <= 1) {
+ // Should never occur
+ cerr<<"Previous Extract SNP error."<<endl;
+ exit(255);
+ return -1;
+ }
+ char t_base = (ref&0x3);
+ for(allele1=0;allele1!=4;allele1++) {
+ for(allele2=allele1;allele2!=4;allele2++) {
+ if (! snp->is_hapmap()) {
+ if(snp->get_freq(allele1)>0 && snp->get_freq(allele2)>0) {
+ // Here the frequency is just a tag to indicate SNP alleles in non-HapMap sites
+ if(allele1 == allele2 && allele1 == t_base) {
+ // refHOM
+ real_p_prior[allele1<<2|allele2] = 1;
+ }
+ else if (allele1 == t_base || allele2 == t_base) {
+ // refHET: 1 ref 1 alt
+ real_p_prior[allele1<<2|allele2] = snp->is_validated()?para->het_val_r:para->het_unval_r;
+ }
+ else if (allele1 == allele2) {
+ real_p_prior[allele1<<2|allele2] = snp->is_validated()?para->althom_val_r:para->althom_unval_r;
+ }
+ else {
+ // altHET: 2 diff alt base
+ real_p_prior[allele1<<2|allele2] = snp->is_validated()?para->het_val_r:para->het_unval_r;
+ }
+ }
+ }
+ else {
+ // Real HapMap Sites
+ if(snp->get_freq(allele1)>0 && snp->get_freq(allele2)>0) {
+ real_p_prior[allele1<<2|allele2] = (allele1==allele2?1:(2*para->het_val_r))*snp->get_freq(allele1)*snp->get_freq(allele2);
+ }
+ }
+ //cerr<<"ACTG"[t_base]<<"\t"<<"ACTG"[allele1]<<"ACTG"[allele2]<<"\t"<<p_prior[t_base<<4|allele1<<2|allele2]<<endl;
+ }
+ }
+ return 1;
+}
diff --git a/rank_sum.cc b/rank_sum.cc
new file mode 100644
index 0000000..249099d
--- /dev/null
+++ b/rank_sum.cc
@@ -0,0 +1,128 @@
+#include "soap_snp.h"
+
+int Prob_matrix::rank_table_gen() {
+ // When N <= 63, (so that n1<=31), use this table to test
+ ubit64_t i, n1, N, T1;
+ rate_t p_left, p_right;
+
+ // Calculate the factorials
+ double * fact = new double [64];
+ fact[0]=(double)1.0;
+ for(i=1;i!=64;i++) {
+ fact[i] = fact[i-1]*i;
+ }
+
+ ubit64_t * rank_sum= new ubit64_t [64*64*2048]; // 6bit: N; 5bit: n1; 11bit; T1
+ memset(rank_sum, 0, sizeof(ubit64_t)*64*64*2048);
+ rank_sum[0]=1;
+ for(N=1;N!=64;N++) {
+ //cerr<<N<<endl;
+ for(n1=0;n1<=N;n1++) {
+ //cerr<<n1<<endl;
+ for(T1=(1+n1)*n1/2;T1<=(N+N-n1+1)*n1/2;T1++) {
+ //cerr<<T1<<endl;
+ // Dynamic programming to generate the table
+ rank_sum[N<<17|n1<<11|T1] = rank_sum[((N-1)<<17)|(n1<<11)|T1] + ((T1>=N && n1>0) ? rank_sum[((N-1)<<17)|((n1-1)<<11)|(T1-N)]:0);
+ // Here, the p_rank is not cumulative
+ p_rank[(N<<17)|(n1<<11)|T1] = rank_sum[N<<17|n1<<11|T1] / (fact[N]/(fact[n1]*fact[N-n1]));
+ //cerr<<p_rank[(N<<17)|(n1<<11)|T1]<<endl;
+ }
+ p_left = 0.0, p_right =1.0;
+ for(T1=(1+n1)*n1/2;T1<=(N+N-n1+1)*n1/2;T1++) {
+ p_right = 1.0 - p_left;
+ p_left += p_rank[(N<<17)|(n1<<11)|T1];
+ p_rank[N<<17|n1<<11|T1] = (p_left<p_right?p_left:p_right);
+ //std::cerr<<N<<"\t"<<n1<<"\t"<<T1<<"\t"<<p_rank[(N<<17)|(n1<<11)|T1]<<endl;
+ }
+ }
+ }
+ delete [] rank_sum;
+ delete [] fact;
+ return 1;
+}
+
+double Call_win::normal_test(int n1, int n2, double T1, double T2) {
+ double u1, u2;
+ u1 = (T1 - n1*(n1+n2+1)/2) / sqrt(n1*n2*(n1+n2+1)/(double)12);
+ u2 = (T2 - n2*(n1+n2+1)/2) / sqrt(n1*n2*(n1+n2+1)/(double)12);
+ return normal_value(fabs(u1)>fabs(u2)?u1:u2);
+}
+
+double Call_win::table_test(double *p_rank, int n1, int n2, double T1, double T2) {
+ if(n1<=n2) {
+ return p_rank[(n1+n2)<<17|n1<<11|(int)(T1)]+(T1-(int)T1)*(p_rank[(n1+n2)<<16|n1<<11|(int)(T1+1)]-p_rank[(n1+n2)<<17|n1<<11|(int)(T1)]);
+ }
+ else {
+ return p_rank[(n1+n2)<<17|n2<<11|(int)(T2)]+(T2-(int)T2)*(p_rank[(n1+n2)<<16|n2<<11|(int)(T2+1)]-p_rank[(n1+n2)<<17|n2<<11|(int)(T2)]);
+ }
+}
+
+double Call_win::rank_test(Pos_info & info, char best_type, double * p_rank, Parameter * para) {
+ if( (best_type&3) == ((best_type>>2)&3) ) {
+ // HOM
+ return 1.0;
+ }
+ if( info.count_uni[best_type&3]==0 || info.count_uni[(best_type>>2)&3]==0) {
+ // HET with one allele...
+ return 0.0;
+ }
+ //cerr<<"RankSum:"<<info.pos<<endl;
+ //int * same_qual_count = new int [para->q_max-para->q_min+1];
+ //memset(same_qual_count, 0, sizeof(int)*(para->q_max-para->q_min+1));
+ //double * rank_array= new double [para->q_max-para->q_min+1];
+ //memset(rank_array, 0, sizeof(double)*(para->q_max-para->q_min+1));
+ int *same_qual_count = new int [64];
+ double *rank_array = new double [64];
+ memset(same_qual_count,0,sizeof(int)*64);
+ memset(rank_array,0,sizeof(double)*64);
+
+ int rank(0);
+ double T[4]={0.0, 0.0, 0.0, 0.0};
+ bool is_need[4] ={false,false,false,false};
+ is_need[(best_type&3)]=true; is_need[((best_type>>2)&3)]=true;
+ std::string::size_type o_base, strand;
+ int q_score, coord;
+ for(o_base=0;o_base!=4;o_base++) {
+ if(info.count_uni[o_base]==0 || !is_need[o_base]) continue;
+ for(q_score=para->q_max-para->q_min;q_score>=0;q_score--) {
+ for(coord=para->read_length-1;coord>=0;coord--) {
+ for(strand=0;strand<2;strand++) {
+ same_qual_count[q_score] += info.base_info[o_base<<15|strand<<14|q_score<<8|coord];
+ //if(info.pos==1256 && info.base_info[o_base<<13|strand<<12|q_score<<6|coord]!=0) {
+ // cerr<<info.pos<<"\t"<<q_score<<"\t"<<same_qual_count[q_score]<<"\t"<<int(info.base_info[o_base<<13|strand<<12|q_score<<6|coord])<<endl;
+ //}
+ }
+ }
+ }
+ }
+ rank = 0;
+ for(q_score=0;q_score<=(ubit64_t)(para->q_max-para->q_min+1);q_score++) {
+ rank_array[q_score]= rank+(1+same_qual_count[q_score])/2.0;
+ rank += same_qual_count[q_score];
+ }
+ for(o_base=0;o_base!=4;o_base++) {
+ if(info.count_uni[o_base]==0 || !is_need[o_base]) continue;
+ for(q_score=para->q_max-para->q_min;q_score>=0;q_score--) {
+ for(coord=para->read_length-1;coord>=0;coord--) {
+ for(strand=0;strand<2;strand++) {
+ //cerr<<"ACTG"[o_base]<<endl;
+ T[o_base] += (rank_array[q_score] * info.base_info[o_base<<15|strand<<14|q_score<<8|coord]);
+ //cerr<<T[o_base]<<endl;
+ }
+ }
+ }
+ }
+ delete [] same_qual_count;
+ delete [] rank_array;
+ //for(size_t a=0;a!=4;a++) {
+ // fprintf(stderr, "%lf\t", T[a]);
+ //}
+ //fprintf(stderr, "\n");
+ //std::cerr<<"%d\t%d\t%lf\t%lf", info.count_uni[best_type&3], info.count_uni[(best_type>>2)&3], T[best_type&3], T[(best_type>>2)&3]);
+ if (info.count_uni[best_type&3]+info.count_uni[(best_type>>2)&3]<64) {
+ return table_test(p_rank, info.count_uni[best_type&3], info.count_uni[(best_type>>2)&3], T[best_type&3], T[(best_type>>2)&3]);
+ }
+ else {
+ return normal_test(info.count_uni[best_type&3], info.count_uni[(best_type>>2)&3],T[best_type&3], T[(best_type>>2)&3]);
+ }
+}
diff --git a/readme b/readme
new file mode 100644
index 0000000..5a1220d
--- /dev/null
+++ b/readme
@@ -0,0 +1,139 @@
+Program: SOAPsnp (Short Oligonucleotide Analysis Package for Single Nucleotide Polymorphism)
+
+Copyright (C) 2008, BGI Shenzhen.
+
+License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
+This is free software: you are free to change and redistribute it.
+There is NO WARRANTY, to the extent permitted by law.
+
+Author: BGI shenzhen
+Contact: soap at genomics.org.cn
+
+Introduction
+
+SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). Despite its name, the program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference. The SNPs can then be identified on the consensus sequence through the comparison with the reference. In the first Asian genome re-sequencing project, evalution of SOAPsnp result on Illumina HapMap 1M Bea [...]
+
+SOAPsnp uses a method based on Bayesa' theorem (the reverse probability model) to call consensus genotype by carefully considering the data quality, alignment, and recurring experimental errors. All these kinds of information was integrated into a single quality score for each base in PHRED scale to measure the accuracy of consensus calling. Currently, it supports the alignment format of SoapMap.
+
+Download
+
+<Download link>
+
+System requirements
+SOAPsnp is a command line driven program written in C/C++ that generally runs under 64-bit Linux system. The program has been tested on various platforms like x86-64 Xeon with Linux kernel 2.6.9 and Loongson 2E/2F with Linux kernel 2.6.22. It is in principle portable to other architectures/systems as only standard C++ libraries were used. GNU Compiler Collection (version>=3.4) is recommended to compile the codes.
+
+The program needs ~500M or even smaller memory to run. However, its output might be very large that consumes a lot of harddisk space. In text output mode, the output file may be as large as 60 times the genome size (e.g. 180G free space is required to run a human genome). In GLF output format (which is proposed by Prof. R. Durbin in Wellcome Trust Sanger Institute), the output file approximately requires a free disk space of 12 times the genome size to store.
+
+Installation
+1. Download the tarball of the latest SOAPsnp version from the link above. (For example, SOAPsnp.tar.gz)
+2. In the Linux console:
+tar zxvf /<PATH_WHERE_YOU_PUT_THE_TARBALL>/SOAPsnp.tar.gz
+cd SOAPsnp/
+3. Change the 'makefile' if necessary. For example, you may would like to modify the compiler optimization parameters.
+4. In the Linux console:
+make all
+Then an executable of SOAPsnp will be generated in the directory.
+In the Linux console, type:
+./soapsnp
+or:
+<Absolute path>/soapsnp
+ to run the program. You may copy the executable to /usr/bin/ or other system paths defined in the environment variables so that you can simply run the program by directly typing 'soapsnp' in the console.
+
+Quick Start:
+For diploid genome resequencing:
+soapsnp -i <Alignment.soap.sort.chrN> -d <chrN.fasta> -o <chrN.consensus> -r 0.00005 e 0.0001 -t -u -L <Maximum Read Length> -M <chrN.mat>
+
+For monoploid genome resequencing:
+soapsnp -i <Alignment.soap.sort.chrN> -d <chrN.fasta> -o <chrN.consensus> -r 0.0001 -t -u -L <Maximum Read Length> -M <chrN.mat> -m
+
+Usage
+Command line options:
+1. Required parameters:
+-i <FILE> Input SORTED SOAPaligner(soap) alignment result
+Note that here we say 'sorted' means alignments of each chromosome are sorted first by chromosome name lexicographically and then by coordinates on each chromosome numerically.
+
+-d <FILE> Reference DNA sequence in FASTA format
+
+-o <FILE> Output consensus file
+
+2. Optional parameters:(default in [])
+
+-z <Char> ASCII character that stands for quality score==0 [@]
+FASTQ files generated by Illumina base-calling pipeline use '@' as 0, but some institutes use '!' as 0.
+
+-g <Double> Global error dependency coefficient, 0.0(complete dependent)~1.0(complete independent)[0.9]
+
+-p <Double> PCR error dependency coefficient, 0.0(complete dependent)~1.0(complete independent)[0.5]
+Sequencing errors are found slightly repeatable (once an error occur, additional errors also tend to occur) due to various reasons. Therefore, observations of sequencing errors are not complete independent. The main source of repeatable errors is believed to be PCR amplification in sequencing process. The proper values of the two parameters rely on wetlab process. Nonetheless, the default value generally work at most time.
+
+-r <Double> novel altHOM prior probability [0.0005]
+
+-e <Double> novel HET prior probability [0.0010]
+The two are prior probabilities of homozygous SNPs (altHOM) and heterozygous SNPs (HET), which are used in Bayes formula calculation. Note these are prior probabilities of a new (novel) SNP. They are expected to be stringent. For different species, the two values should change if necessary.
+
+-t set transition/transversion ratio to 2:1 in prior probability
+
+-s <FILE> Pre-formatted known SNP information.
+The file consist of a lot of lines like this one:
+chr1 201979756 1 1 0 0.161 0 0 0.839 rs568
+The columns from left to right are: name of chromosome, coordinate on the chromosome, whether the SNP has allele frequency information (1 is true, 0 is false), whether the SNP is validated by experiment (1 is true, 0 is false), whether the SNP is actually an indel (1 is true, 0 is false), frequency of A, frequency of C, frequency of T, frequency of G, SNP id. For known SNP sites that do not have allele frequency information, the frequency information can be arbitrarily determined as any [...]
+
+-2 specify this option will REFINE SNP calling using known SNP information [Off]
+
+-a <Double> Validated HET prior, if no allele frequency known [0.1]
+
+-b <Double> Validated altHOM prior, if no allele frequency known[0.05]
+
+-j <Double> Unvalidated HET prior, if no allele frequency known [0.02]
+
+-k <Double> Unvalidated altHOM rate, if no allele frequency known[0.01]
+The parameters are related to using external SNP information to alter prior probabilities for SNP calling. SOAPsnp will try using allele frequency information as prior probability in calling genotypes for each site. If the allele frequency information is absent, it will use the above 4 parameters as prior probability.
+
+-u Enable rank sum test (that check whether the two allele of a possible HET call have same sequencing quality) to give HET further penalty for better accuracy. [Off]
+
+-n Enable binomial probability calculation (that check whether the two allele are observed equally)to give HET further penalty for better accuracy. [Off]
+
+-m Enable monoploid calling mode, this will ensure all consensus as HOM and you probably should SPECIFY higher altHOM rate. [Off]
+
+-q Only output potential SNPs. Useful in Text output mode. [Off]
+
+-M <FILE> Output the quality calibration matrix; the matrix can be reused with -I if you rerun the program
+
+-I <FILE> Input previous quality calibration matrix. It cannot be used simutaneously with -M
+
+-L <short> maximum length of read [45]
+Please note that once length of some reads exceeds the parameter will probably collapse the program.
+
+-Q <short> maximum FASTQ quality score [40]
+
+-F <int> Output format. 0: Text; 1: GLFv2; 2: GPFv2.[0]
+
+-E <String> Extra headers EXCEPT CHROMOSOME FIELD specified in GLFv2 output. Format is "TypeName1:DataName1:TypeName2:DataName2"[]
+
+-T <FILE> Only call consensus on regions specified in FILE. Format of this file is:
+ChrName\tStart\tEnd
+ChrName\tStart\tEnd
+...
+
+-h Display this help
+
+Output format
+1. Text format
+The result of SOAPsnp has 17 columns:
+1) Chromosome ID
+2) Coordinate on chromosome, start from 1
+3) Reference genotype
+4) Consensus genotype
+5) Quality score of consensus genotype
+6) Best base, average quality score of best base
+7) Count of uniquely mapped best base
+8) Count of all mapped best base
+9) Second best bases, average quality score of second best base
+10) Count of uniquely mapped second best base
+11) Count of all mapped second best base
+12) Sequencing depth of the site, rank sum test p_value
+13) Average copy number of nearby region
+14) Whether the site is a dbSNP.
+2. GLFv2 and GPFv2
+GLFv2 (Genome Likelihood Format v2) is a binary file format proposed by Prof. R. Durbin.
+
diff --git a/release b/release
new file mode 100644
index 0000000..b840459
--- /dev/null
+++ b/release
@@ -0,0 +1,5 @@
+version: SOAPsnpZ
+date: 25 May 2009
+1. a subvertion of SOAPsnp with gziped file IO. You should confirm BOOST
+ iostream library has been installed in your platform at first. And you can
+ learn more about BOOST from http://www.boost.org/ .
diff --git a/soap_snp.h b/soap_snp.h
new file mode 100644
index 0000000..e3de1ac
--- /dev/null
+++ b/soap_snp.h
@@ -0,0 +1,326 @@
+#ifndef SOAP_SNP_HH_
+#define SOAP_SNP_HH_
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <string>
+#include <map>
+#include <vector>
+#include <cmath>
+#include <iomanip>
+#include <cassert>
+#include <boost/iostreams/filtering_streambuf.hpp>
+#include <boost/iostreams/copy.hpp>
+#include <boost/iostreams/filter/gzip.hpp>
+typedef unsigned long long ubit64_t;
+typedef unsigned int ubit32_t;
+typedef double rate_t;
+typedef unsigned char small_int;
+using namespace std;
+const size_t capacity = sizeof(ubit64_t)*8/4;
+const char abbv[17]={'A','M','W','R','M','C','Y','S','W','Y','T','K','R','S','K','G','N'};
+const ubit64_t glf_base_code[8]={1,2,8,4,15,15,15,15}; // A C T G
+const ubit64_t glf_type_code[10]={0,5,15,10,1,3,2,7,6,11};// AA,CC,GG,TT,AC,AG,AT,CG,CT,GT
+const int global_win_size = 1000;
+
+// Some global variables
+class Files {
+public:
+ ifstream soap_result, ref_seq, dbsnp, region;
+ ofstream consensus, baseinfo, o_region;
+ fstream matrix_file;
+ Files(){
+ soap_result.close();
+ ref_seq.close();
+ dbsnp.close();
+ consensus.close();
+ baseinfo.close();
+ matrix_file.close();
+ region.close();
+ o_region.close();
+ };
+};
+
+class Parameter {
+public:
+ char q_min; // The char stands for 0 in fastq
+ char q_max; // max quality score
+ small_int read_length; // max read length
+ bool is_monoploid; // Is it an monoploid? chrX,Y,M in man.
+ bool is_snp_only; // Only output possible SNP sites?
+ bool refine_mode; // Refine prior probability using dbSNP
+ bool rank_sum_mode; // Use rank sum test to refine HET quality
+ bool binom_mode; // Use binomial test to refine HET quality
+ bool transition_dominant; // Consider transition/transversion ratio?
+ int glf_format; // Generate Output in GLF format: New File Definitions! Since May 1, 2009
+ bool region_only; // Only report consensus in specified region
+ std::string glf_header; // Header of GLF format
+ rate_t althom_novel_r, het_novel_r; // Expected novel prior
+ rate_t althom_val_r, het_val_r; // Expected Validated dbSNP prior
+ rate_t althom_unval_r, het_unval_r; // Expected Unvalidated dbSNP prior
+ rate_t global_dependency, pcr_dependency; // Error dependencies, 1 is NO dependency
+// Default onstruction
+ Parameter(){
+ q_min = 64;
+ q_max = 64+40;
+ read_length = 45;
+ is_monoploid = is_snp_only = refine_mode = rank_sum_mode = binom_mode = transition_dominant = region_only =false;
+ glf_format = 0;
+ glf_header = "";
+ althom_novel_r=0.0005, het_novel_r=0.0010;
+ althom_val_r=0.05, het_val_r=0.10;
+ althom_unval_r=0.01, het_unval_r=0.02;
+ global_dependency= log10(0.9), pcr_dependency= log10(0.5); // In Log10 Scale
+ };
+};
+
+class Soap_format {
+ // Soap alignment result
+ std::string read_id, read, qual, chr_name;
+ int hit, read_len, position, mismatch;
+ char ab, strand;
+public:
+ Soap_format(){;};
+ friend std::istringstream & operator>>(std::istringstream & alignment, Soap_format & soap) {
+ alignment>>soap.read_id>>soap.read>>soap.qual>>soap.hit>>soap.ab>>soap.read_len>>soap.strand>>soap.chr_name>>soap.position>>soap.mismatch;
+ //cerr<<soap<<endl;
+ //exit(1);
+ if(soap.mismatch>200) {
+ int indel_pos,indel_len;
+ string temp("");
+ alignment>>indel_pos;
+ indel_len = soap.mismatch-200;
+ for(int i=0; i!=indel_len; i++) {
+ temp = temp+'N';
+ }
+ soap.read = soap.read.substr(0,indel_pos)+temp+soap.read.substr(indel_pos,soap.read_len-indel_pos);
+ soap.qual = soap.qual.substr(0,indel_pos)+temp+soap.qual.substr(indel_pos,soap.read_len-indel_pos);
+ //cerr<<soap<<endl;
+ }
+ else if (soap.mismatch>100) {
+ int indel_pos,indel_len;
+ alignment>>indel_pos;
+ indel_len = soap.mismatch-100;
+ soap.read = soap.read.substr(0,indel_pos) + soap.read.substr(indel_pos+indel_len, soap.read_len-indel_pos-indel_len);
+ soap.qual = soap.qual.substr(0,indel_pos) + soap.qual.substr(indel_pos+indel_len, soap.read_len-indel_pos-indel_len);
+ //cerr<<soap<<endl;
+ }
+ //cerr<<soap.position<<'\t';
+ soap.position -= 1;
+ //cerr<<soap.position<<endl;
+ return alignment;
+ }
+ friend std::ostream & operator<<(std::ostream & o, Soap_format & soap) {
+ o<<soap.read_id<<'\t'<<soap.read<<'\t'<<soap.qual<<'\t'<<soap.hit<<'\t'<<soap.ab<<'\t'<<soap.read_len<<'\t'<<soap.strand<<'\t'<<soap.chr_name<<'\t'<<soap.position<<'\t'<<soap.mismatch;
+ return o;
+ }
+ char get_base(std::string::size_type coord) {
+ return read[coord];
+ }
+ char get_qual(std::string::size_type coord) {
+ return qual[coord];
+ }
+ bool is_fwd(){
+ return (strand=='+');
+ }
+ int get_read_len(){
+ return read_len;
+ }
+ inline int get_pos(){
+ return position;
+ }
+ std::string get_chr_name(){
+ return chr_name;
+ }
+ int get_hit(){
+ return hit;
+ }
+ bool is_unique(){
+ return (hit==1);
+ }
+ bool is_N(int coord) {
+ return (read[coord] == 'N');
+ }
+};
+
+// dbSNP information
+class Snp_info {
+ bool validated;
+ bool hapmap_site;
+ bool indel_site;
+ rate_t * freq; // Arrary of 4 elements recording frequency of ACTG
+public:
+ Snp_info(){
+ validated=hapmap_site=indel_site=false;
+ freq = new rate_t [4];
+ memset(freq,0,sizeof(rate_t)*4);
+ }
+ Snp_info(const Snp_info & other) {
+ validated = other.validated;
+ hapmap_site = other.hapmap_site;
+ indel_site = other.indel_site;
+ freq = new rate_t [4];
+ memcpy(freq, other.freq, sizeof(rate_t)*4);
+ }
+ ~Snp_info(){
+ delete [] freq;
+ }
+ friend std::istringstream& operator>>(std::istringstream & s, Snp_info & snp_form) {
+ s>>snp_form.hapmap_site>>snp_form.validated>>snp_form.indel_site>>snp_form.freq[0]>>snp_form.freq[1]>>snp_form.freq[2]>>snp_form.freq[3];
+ return s;
+ }
+ Snp_info & operator=(Snp_info& other) {
+ this->validated = other.validated;
+ this->hapmap_site = other.hapmap_site;
+ this->indel_site = other.indel_site;
+ this->freq = new rate_t [4];
+ memcpy(this->freq, other.freq, sizeof(rate_t)*4);
+ return *this;
+
+ }
+ bool is_validated(){
+ return validated;
+ }
+ bool is_hapmap(){
+ return hapmap_site;
+ }
+ bool is_indel(){
+ return indel_site;
+ }
+ rate_t get_freq(char bin_base_2bit) {
+ return freq[bin_base_2bit];
+ }
+};
+
+// Chromosome(Reference) information
+class Chr_info {
+ ubit32_t len;
+ ubit64_t* bin_seq; // Sequence in binary format
+ ubit64_t* region_mask;
+ ubit64_t* region_win_mask;
+ // 4bits for one base: 1 bit dbSNPstatus, 1bit for N, followed two bit of base A: 00, C: 01, T: 10, G:11,
+ // Every ubit64_t could store 16 bases
+ map<ubit64_t, Snp_info*> dbsnp;
+public:
+ Chr_info(){
+ len = 0;
+ bin_seq = NULL;
+ region_mask = NULL;
+ region_win_mask = NULL;
+ };
+ Chr_info(const Chr_info & other);
+ ~Chr_info(){
+ delete [] bin_seq;
+ delete [] region_mask;
+ delete [] region_win_mask;
+ }
+ ubit32_t length() {
+ return len;
+ }
+ ubit64_t get_bin_base(std::string::size_type pos) {
+ return (bin_seq[pos/capacity]>>(pos%capacity*4))&0xF; // All 4 bits
+ }
+ int binarize(std::string & seq);
+ int insert_snp(std::string::size_type pos, Snp_info & new_snp);
+ int region_mask_ini();
+ bool is_in_region(std::string::size_type pos) {
+ return ((region_mask[pos/64]>>(63-pos%64))&1);
+ }
+ bool is_in_region_win(std::string::size_type pos) {
+ pos /= global_win_size; // Calculate in which windows the site is
+ //cerr<<pos<<endl;
+ //exit(1);
+ return ((region_win_mask[pos/64]>>(63-pos%64))&1);
+ }
+ int set_region(int start, int end);
+ Snp_info * find_snp(ubit64_t pos) {
+ return dbsnp.find(pos)->second;
+ }
+ ubit64_t * get_region() {
+ return region_mask;
+ }
+};
+
+typedef std::string Chr_name;
+class Genome {
+public:
+ map<Chr_name, Chr_info*> chromosomes;
+
+ Genome(ifstream & fasta, ifstream & known_snp);
+ ~Genome();
+
+ bool add_chr(Chr_name &);
+ int read_region(std::ifstream & region, Parameter * para);
+};
+
+class Prob_matrix {
+public:
+ rate_t *p_matrix, *p_prior; // Calibration matrix and prior probabilities
+ rate_t *base_freq, *type_likely, *type_prob; // Estimate base frequency, conditional probability, and posterior probablity
+ rate_t *p_rank, *p_binom; // Ranksum test and binomial test on HETs
+ Prob_matrix();
+ ~Prob_matrix();
+ int matrix_gen(std::ifstream & alignment, Parameter * para, Genome * genome);
+ int matrix_read(std::fstream & mat_in, Parameter * para);
+ int matrix_write(std::fstream & mat_out, Parameter * para);
+ int prior_gen(Parameter * para);
+ int rank_table_gen();
+
+};
+
+class Pos_info {
+public:
+ unsigned char ori;
+ small_int *base_info;
+ int pos, *count_uni, *q_sum, depth, dep_uni, repeat_time, *count_all;
+
+ Pos_info(){
+ ori = 0xFF;
+ base_info = new small_int [4*2*64*256]; // base info : 4x2x64x64 matrix, base x strand x qual x read_pos
+ memset(base_info,0,sizeof(small_int)*4*2*64*256);
+ pos = -1;
+ count_uni = new int [4]; // Count of unique bases
+ memset(count_uni,0,sizeof(int)*4);
+ q_sum = new int [4]; // Sum of quality of unique bases
+ memset(q_sum,0,sizeof(int)*4);
+ depth = 0;
+ dep_uni = 0;
+ repeat_time = 0;
+ count_all = new int [4]; // Count of all bases
+ memset(count_all,0,sizeof(int)*4);
+ }
+ ~Pos_info(){
+ delete [] base_info;
+ delete [] count_uni;
+ delete [] q_sum;
+ delete [] count_all;
+ }
+};
+
+class Call_win {
+public:
+ ubit64_t win_size;
+ ubit64_t read_len;
+ Pos_info * sites;
+ Call_win(ubit64_t read_length, ubit64_t window_size=global_win_size) {
+ sites = new Pos_info [window_size+read_length];
+ win_size = window_size;
+ read_len = read_length;
+ }
+ ~Call_win(){
+ delete [] sites;
+ }
+
+ int initialize(ubit64_t start);
+ int deep_init(ubit64_t start);
+ int recycle();
+ int call_cns(Chr_name call_name, Chr_info* call_chr, ubit64_t call_length, Prob_matrix * mat, Parameter * para, std::ofstream & consensus, std::ofstream & baseinfo);
+ int soap2cns(std::ifstream & alignment, std::ofstream & consensus, std::ofstream & baseinfo, Genome * genome, Prob_matrix * mat, Parameter * para);
+ int snp_p_prior_gen(double * real_p_prior, Snp_info* snp, Parameter * para, char ref);
+ double rank_test(Pos_info & info, char best_type, double * p_rank, Parameter * para);
+ double normal_value(double z);
+ double normal_test(int n1, int n2, double T1, double T2);
+ double table_test(double *p_rank, int n1, int n2, double T1, double T2);
+};
+
+#endif /*SOAP_SNP_HH_*/
--
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