make htslib location configurable

Makefile.am

@@ -3,7 +3,7 @@
 ## to provide a way for the user to supply additional arguments.
 ACLOCAL_AMFLAGS = -I m4 ${ACLOCAL_FLAGS}
 
-AM_CPPFLAGS = -fopenmp -I ../htslib/ -I ../../htslib/htslib -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 
+AM_CPPFLAGS = -fopenmp -pipe -D__STDC_LIMIT_MACROS -Wall -Wno-unused-local-typedefs -Wno-enum-compare -fpic -O2 
 
 noinst_HEADERS = \
 	Constant.h pException.h \
@@ -24,4 +24,4 @@ demuxlet_SOURCES = \
 	tsv_reader.cpp \
 	cmd_cram_demuxlet.cpp
 
-demuxlet_LDADD = ../htslib/libhts.a -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto
+demuxlet_LDADD = -lhts -lpthread -llzma -lz -lbz2 -lgomp -lcurl -lcrypto

README.md

@@ -8,9 +8,7 @@ Genetic multiplexing of barcoded single cell RNA-seq
 
 ### Installing demuxlet
 
-Before installing demuxlet, you need to install [htslib](https://github.com/samtools/htslib) in the same directory you want to install demuxlet (i.e. demuxlet and htslib should be siblings).
-
-After installing htslib, you can clone the current snapshot of this repository to install as well
+Before installing demuxlet, you need to install [htslib](https://github.com/samtools/htslib). If you do not install this to standard system paths, you'll need to pass the directory for header files and compiled library file to configure. For example, if you downloaded and compiled htslib in `/opt/htslib`, run `./configure CPPFLAGS=-I/opt/htslib LDFLAGS=-L/opt/htslib`.
 
 <pre>
 $ git clone https://github.com/statgen/demuxlet.git

configure.ac

@@ -17,6 +17,8 @@ AC_CONFIG_MACRO_DIR([m4])
 AC_PROG_CXX
 
 AC_CHECK_HEADERS([limits.h stddef.h stdint.h stdlib.h string.h unistd.h])
+AC_CHECK_HEADERS([htslib/kseq.h htslib/kstring.h htslib/khash.h htslib/hts.h htslib/sam.h],
+		 [], [AC_MSG_ERROR([htslib headers not found. Please download and compile, and pass CPPFLAGS=-I<htslib_path>])])
 
 AC_HEADER_STDBOOL
 AC_C_INLINE
@@ -38,6 +40,7 @@ AC_FUNC_REALLOC
 AC_FUNC_STRTOD
 AC_CHECK_FUNCS([floor gethostname memset pow select sqrt strchr strstr strtol])
 AC_CHECK_LIB(z, gzopen, [], [AC_MSG_ERROR([libz.{so,a} was not found. Please install zlib at http://www.zlib.net/ first])])
+AC_CHECK_LIB(hts, hts_open, [], [AC_MSG_ERROR([libhts.{so,a} was not found. Please download and compile htslib and pass LDFLAGS=-L<htslib_path>])])
 AC_CHECK_LIB([m],[erf],[AC_DEFINE([HAVE_ERF],[1],[libm includes erf])])
 AC_CHECK_LIB([m],[erfc],[AC_DEFINE([HAVE_ERFC],[1],[libm includes erfc])])
 

supplementary.material/s15_interferon_comparison/demuxlet_interferon_comparison.R

@@ -0,0 +1,21 @@
+library(ggplot2);
+library(data.table);
+
+t <- fread("t.ifn.txt");
+##t.timecourse <- fread("t.ifn.timecourse.txt")
+##t.timecourse <- cbind(t.timecourse[,c(1,2)],t.timecourse[,c(14)]-t.timecourse[,c(13)]);
+dc <- fread("dc.ifn.txt");
+
+dc.small <- dc[match(t$gene,dc$"#gene"),];
+
+cors <- NULL;
+
+cd4.dscrnaseq <- fread("cd4.dscrnaseq.txt");
+cd4.matched <- intersect(cd4.dscrnaseq$featureData.symbol, dc.small$"#gene")
+
+cors[1,1] <- cor(cd4.dscrnaseq$log2FoldChange[match(cd4.matched,cd4.dscrnaseq$featureData.symbol)], dc.small$log2FoldChange[match(cd4.matched, dc.small$"#gene")])
+
+dc.dscrnaseq <- fread("dc.dscrnaseq.txt");
+dc.matched <- intersect(dc.dscrnaseq$featureData.symbol, dc.small$"#gene")
+
+cors[1,2] <- cor(dc.dscrnaseq$log2FoldChange[match(dc.matched,dc.dscrnaseq$featureData.symbol)], dc.small$log2FoldChange[match(dc.matched, dc.small$"#gene")])

supplementary.material/s15_interferon_comparison/mega.dscrnaseq.txt

@@ -0,0 +1 @@
+	baseMean	log2FoldChange	lfcSE	stat	pvalue	padj	featureData.symbolENSG00000172183	48.73971611	3.39943504	0.25673477	13.24103875	5.08E-40	2.01E-36	ISG20ENSG00000126709	24.63069689	4.729285886	0.411285862	11.49878058	1.34E-30	2.64E-27	IFI6ENSG00000160932	20.11198964	3.73477673	0.337708262	11.0591808	1.98E-28	2.61E-25	LY6EENSG00000187608	101.5522042	4.72273018	0.432079813	10.93022641	8.26E-28	8.17E-25	ISG15ENSG00000119917	24.21175382	5.052054389	0.481616847	10.48977922	9.63E-26	7.61E-23	IFIT3ENSG00000157601	12.90083429	4.998116804	0.554855165	9.007966615	2.10E-19	1.38E-16	MX1ENSG00000134321	10.42903782	5.65015929	0.73725106	7.663819825	1.80E-14	1.02E-11	RSAD2ENSG00000121858	11.84628308	4.057294516	0.552837112	7.339041521	2.15E-13	1.06E-10	TNFSF10ENSG00000133106	7.946588797	4.07340926	0.556957177	7.31368483	2.60E-13	1.14E-10	EPSTI1ENSG00000169245	30.66831969	5.564708518	0.764814498	7.275893082	3.44E-13	1.36E-10	CXCL10ENSG00000188313	8.681161343	2.979494563	0.415163723	7.17667368	7.14E-13	2.57E-10	PLSCR1ENSG00000156587	9.733564681	2.573846699	0.362441617	7.101410475	1.23E-12	4.07E-10	UBE2L6ENSG00000089127	7.740013379	3.279695818	0.480660802	6.823306173	8.90E-12	2.70E-09	OAS1ENSG00000137959	6.450226063	3.718666015	0.549067599	6.772692505	1.26E-11	3.57E-09	IFI44LENSG00000125148	6.611203492	3.968875048	0.600587291	6.608323402	3.89E-11	1.02E-08	MT2AENSG00000135114	7.797273462	3.15573061	0.480512375	6.567428379	5.12E-11	1.26E-08	OASLENSG00000185745	20.3780089	4.271929722	0.656406659	6.508053603	7.61E-11	1.77E-08	IFIT1ENSG00000240065	16.41579856	1.798230174	0.277767747	6.473862403	9.55E-11	2.10E-08	PSMB9ENSG00000205413	6.687311679	2.67631246	0.42649018	6.275203007	3.49E-10	7.26E-08	SAMD9ENSG00000142089	12.10924008	3.418210733	0.551324063	6.200002803	5.65E-10	1.12E-07	IFITM3ENSG00000185507	8.781810582	2.626984654	0.43241254	6.075181476	1.24E-09	2.33E-07	IRF7ENSG00000055332	5.06353145	3.437905896	0.583054241	5.896374045	3.72E-09	6.67E-07	EIF2AK2ENSG00000107201	4.483612329	3.844543346	0.657036435	5.851339656	4.88E-09	8.38E-07	DDX58ENSG00000183486	4.041015134	3.830346286	0.659122142	5.811284497	6.20E-09	1.02E-06	MX2ENSG00000108700	19.6463042	5.071794482	0.899645659	5.637546771	1.72E-08	2.73E-06	CCL8ENSG00000134326	4.435075567	3.817926508	0.686341921	5.562717926	2.66E-08	3.89E-06	CMPK2ENSG00000213689	2.870206797	4.741620781	0.851422815	5.569055348	2.56E-08	3.89E-06	TREX1ENSG00000185201	6.652611439	2.333542686	0.420217274	5.553181251	2.81E-08	3.96E-06	IFITM2ENSG00000117228	6.160860921	2.911080756	0.527325452	5.520463211	3.38E-08	4.61E-06	GBP1ENSG00000137965	3.619474403	3.296805088	0.599006334	5.503790029	3.72E-08	4.90E-06	IFI44ENSG00000115415	4.509332598	2.643668696	0.481574143	5.489640034	4.03E-08	5.13E-06	STAT1ENSG00000138646	4.495232325	3.371305646	0.619260896	5.444079658	5.21E-08	6.43E-06	HERC5ENSG00000146425	8.834610853	2.030768626	0.373721818	5.433904384	5.51E-08	6.60E-06	DYNLT1ENSG00000177409	5.105110951	3.544971069	0.654435156	5.416840825	6.07E-08	6.93E-06	SAMD9LENSG00000100911	14.8268164	1.638352942	0.302573119	5.41473395	6.14E-08	6.93E-06	PSME2ENSG00000131203	4.321890455	4.756715168	0.883825441	5.381962263	7.37E-08	8.09E-06	IDO1ENSG00000130066	55.54995169	1.448399687	0.272214637	5.320800178	1.03E-07	1.10E-05	SAT1ENSG00000163565	6.851409661	2.093501497	0.398008942	5.259935836	1.44E-07	1.50E-05	IFI16ENSG00000067066	5.96582398	2.020997991	0.399010393	5.065025938	4.08E-07	4.14E-05	SP100ENSG00000111640	34.62480758	-1.04534994	0.208636225	-5.010395198	5.43E-07	5.37E-05	GAPDHENSG00000173193	3.068726407	3.18249938	0.638508478	4.984271141	6.22E-07	5.85E-05	PARP14ENSG00000163644	3.736232245	2.424995639	0.486343847	4.986175219	6.16E-07	5.85E-05	PPM1KENSG00000169429	6.219417301	-3.549534254	0.714075064	-4.970813901	6.67E-07	6.13E-05	IL8ENSG00000188404	10.26950942	1.725786952	0.348989611	4.945095493	7.61E-07	6.84E-05	SELLENSG00000002549	3.866956855	2.719983981	0.556058749	4.891540664	1.00E-06	8.79E-05	LAP3ENSG00000132274	2.193367506	3.544494809	0.730049577	4.855142608	1.20E-06	0.000103354	TRIM22ENSG00000068079	4.107445383	2.872945737	0.594009257	4.836533609	1.32E-06	0.000111096	IFI35ENSG00000185338	5.834513859	1.967416342	0.40789967	4.823284951	1.41E-06	0.000116265	SOCS1ENSG00000013374	3.441384666	2.686558431	0.557959482	4.814970473	1.47E-06	0.000118739	NUB1ENSG00000111331	1.822637755	4.205477831	0.87608595	4.80030279	1.58E-06	0.00012522	OAS3ENSG00000135535	6.798313544	1.595455131	0.345208911	4.621709006	3.81E-06	0.000294921	CD164ENSG00000169248	3.342401742	4.230823359	0.92007922	4.598325087	4.26E-06	0.000323685	CXCL11ENSG00000086065	5.013119215	1.990929994	0.441060296	4.513963311	6.36E-06	0.000474443	CHMP5ENSG00000179144	14.3719283	1.657648763	0.372139864	4.454370313	8.41E-06	0.000615778	GIMAP7ENSG00000132530	2.959685847	2.49713802	0.565806914	4.413410225	1.02E-05	0.000731155	XAF1ENSG00000115267	2.284687174	3.060183133	0.714952393	4.280261403	1.87E-05	0.001317385	IFIH1ENSG00000139278	2.897761782	-2.204863702	0.523308857	-4.213312414	2.52E-05	0.001744791	GLIPR1ENSG00000162654	3.198380711	2.838593233	0.680239707	4.172930811	3.01E-05	0.002030665	GBP4ENSG00000204264	7.691877156	1.546689863	0.370812915	4.171078733	3.03E-05	0.002030665	PSMB8ENSG00000196141	1.188607163	3.738800257	0.904007382	4.135807219	3.54E-05	0.002329764	SPATS2LENSG00000136514	1.863306282	2.889238657	0.706976405	4.086754011	4.37E-05	0.002834106	RTP4ENSG00000128383	8.420836588	3.086623664	0.757916509	4.072511455	4.65E-05	0.002964568	APOBEC3AENSG00000138035	1.484215153	3.02499475	0.756764004	3.997276208	6.41E-05	0.004019468	PNPT1ENSG00000143106	5.767253199	1.490137902	0.3744416	3.979627	6.90E-05	0.0042622	PSMA5ENSG00000092010	10.26079587	1.005743678	0.253090774	3.973845673	7.07E-05	0.004299861	PSME1ENSG00000122643	8.321556853	1.322735774	0.333617999	3.964821382	7.35E-05	0.004398152	NT5C3AENSG00000102524	3.524721508	2.803084672	0.707693785	3.960872248	7.47E-05	0.004404798	TNFSF13BENSG00000136689	1.853094671	3.692069861	0.940589217	3.925273428	8.66E-05	0.005034806	IL1RNENSG00000197536	2.370267583	2.445052812	0.626397951	3.903353786	9.49E-05	0.005433649	C5orf56ENSG00000059588	1.088203453	3.53356594	0.91520194	3.860968586	0.000112938	0.006224951	TARBP1ENSG00000119922	14.8369318	2.955764786	0.765264544	3.862409163	0.000112274	0.006224951	IFIT2ENSG00000130813	1.978268712	2.570299193	0.665889175	3.859950406	0.00011341	0.006224951	C19orf66ENSG00000117091	5.970060497	1.440755445	0.376441327	3.827304131	0.000129554	0.007013685	CD48ENSG00000034510	43.84150724	1.156682477	0.30262497	3.822164703	0.000132285	0.007064749	TMSB10ENSG00000135899	2.67797177	1.979446683	0.523978856	3.777722444	0.000158269	0.008339728	SP110ENSG00000152558	7.701416431	1.207587938	0.320057835	3.773030387	0.000161277	0.008372113	TMEM123ENSG00000140511	1.095714482	3.471082413	0.92066411	3.770194119	0.000163121	0.008372113	HAPLN3ENSG00000125826	3.123542671	1.758960871	0.481605461	3.652285972	0.000259916	0.01300239	RBCK1ENSG00000185885	1.475047169	2.79428762	0.769689469	3.630409058	0.000282972	0.013752646	IFITM1ENSG00000173821	2.615849181	2.021308438	0.557103495	3.628245838	0.000285353	0.013752646	RNF213ENSG00000069493	4.703248933	1.58588872	0.439101395	3.611668598	0.000304233	0.014485899	CLEC2DENSG00000177721	2.616236055	2.191133326	0.609017048	3.597819359	0.000320896	0.01509741	ANXA2RENSG00000160710	2.000459945	2.24033653	0.63343536	3.536803705	0.000405001	0.018689008	ADARENSG00000130589	1.492260108	2.980991591	0.843111789	3.535701471	0.000406694	0.018689008	HELZ2ENSG00000145287	3.666647003	1.937157064	0.55148223	3.512637325	0.000443683	0.01989713	PLAC8ENSG00000136147	2.129921595	2.187861635	0.623320453	3.510010979	0.000448088	0.01989713	PHF11ENSG00000152778	1.592899836	2.373365941	0.679099658	3.494871356	0.00047429	0.020826614	IFIT5ENSG00000181381	2.293197952	2.137336747	0.617046067	3.463820391	0.000532562	0.023128406	DDX60LENSG00000138642	1.084338138	2.920444677	0.847144946	3.447396684	0.000566017	0.024314115	HERC6ENSG00000175550	9.042783905	1.104327863	0.322376705	3.425582082	0.000613484	0.026069752	DRAP1ENSG00000133574	4.27764425	1.745306992	0.510300882	3.420152805	0.00062586	0.02631274	GIMAP4ENSG00000143546	5.332494965	-2.635022141	0.786709042	-3.349423994	0.000809798	0.033336672	S100A8ENSG00000108771	1.140618522	2.820655148	0.847752909	3.327213766	0.000877191	0.035016738	DHX58ENSG00000134198	1.338582172	-2.94279778	0.891744647	-3.300045353	0.000966692	0.03820367	TSPAN2ENSG00000154451	1.638483755	2.329239385	0.708420191	3.287934783	0.001009252	0.039490738	GBP5ENSG00000138496	1.94652127	2.139330732	0.654485197	3.268722868	0.001080341	0.041505163	PARP9ENSG00000136213	2.316186108	1.796736613	0.549736976	3.268356852	0.001081739	0.041505163	CHST12ENSG00000167996	871.619035	-1.089440854	0.336476563	-3.237791198	0.001204589	0.044910728	FTH1ENSG00000054654	2.376147694	1.912580847	0.593841105	3.22069461	0.001278803	0.04679473	SYNE2ENSG00000116663	1.062998503	2.547604007	0.795270126	3.203444873	0.00135794	0.048787093	FBXO6ENSG00000162645	6.51283022	1.287783169	0.4040219	3.187409317	0.001435535	0.050205601	GBP2ENSG00000168899	2.869226813	2.356081019	0.738967134	3.188343448	0.001430905	0.050205601	VAMP5ENSG00000126353	19.43673347	1.040584759	0.326202671	3.189994604	0.001422755	0.050205601	CCR7ENSG00000123609	4.064529312	1.457454853	0.468189103	3.112961927	0.001852199	0.063651225	NMIENSG00000168961	1.718205523	2.008921358	0.648001008	3.100182458	0.001934015	0.065889878	LGALS9ENSG00000111335	1.19488037	2.515129231	0.820462907	3.065500231	0.002173062	0.073401209	OAS2ENSG00000102871	2.613625381	1.857916602	0.614807687	3.021947579	0.00251154	0.083408467	TRADD